VMD-L Mailing List
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Starting: Thu Dec 19 1996 - 11:40:41 CST
Ending: Sat Nov 09 2024 - 23:40:30 CST
- $B:,>k(J $B6Q(J
- Chavent Mathieu
- Y. U. Sasidhar
- #ANG YUN MEI ELISA#
- #WONG CHEE HOW#
- #YEO JINGJIE#
- .
- . Juita
- 04215287d_at_polyu.edu.hk
- 1(484)993-7152 Marty
- 16.zdsmith_at_gmail.com
- 3D SIG
- May 18th, Late abstract submission deadline for 3Dsig Structural Bioinformatics & Computational Biophysics (Wed May 11 2011 - 16:57:22 CDT)
- _at_huji.ac.il
- a a
- A D
- A. Gomez-Sicilia
- A. M. Carmen Prez
- A. M.M
- AA
- Aaron Blanchard, Ph.D.
- Aaron Larsen
- Aaron Oakley
- Aaron Taudt
- Aaron.Oakley_at_csiro.au
- Aashish Bhatt
- AB
- ABEL Stephane
- ABEL Stephane 175950
- RE: Plot the value of the current frame in the Progress Bar for elapsed Time (Thu Dec 02 2010 - 12:15:22 CST)
- Abhijit Ghosh
- Abhijit Muley
- Abhik Ghosh Moulick
- abhik.ghosh_at_bose.res.in
- Abhishek Bagusetty
- ABHISHEK GUPTA
- RE: How to draw a box in VMD and plot the coordinates of the system (Mon Mar 28 2016 - 00:50:24 CDT)
- Abhishek TYAGI
- Abi Ghanem josephine
- abinayar_at_imsc.res.in
- Abolfazl Bayat
- Abolfazl Musavi
- Abramyan, Tigran
- Abu Naser
- accomp lin
- accutone_at_atlsky.com
- Achar, Sid
- achchirangeebi
- Ackad, Edward
- Ada Zhan
- Adam Brenner
- Adam Goler
- Adam Gross
- Adam Kells
- Adam Kraut
- Adam Kubach
- Adam Marcus
- Adam Matěj
- Adelene Sim
- Adelman, Joshua Lev
- adil mughal
- Adilah Hussien
- Aditi Gotkhindikar
- Aditya Padhi
- Adkins, Laura R
- Adrain Koh
- Adrian E. Roitberg
- Adrian Jasiski
- Adrian Kaats
- Adrian Koh
- Adrian Roitberg
- Adrian turjanski
- Adriano Santana Sanchez
- Adupa Vasista
- Re: namd-l: Pair interaction calculation is not supported in CUDA version (Sun Mar 15 2020 - 23:48:52 CDT)
- Afnan Sultan
- Afroditi Maria Zaki
- Agarwal, Silvi
- Agarwal, Silvi
- Agnieszka Sobkiewicz
- agustina_at_cabm.rutgers.edu
- Ahmad Alqaisi
- Ahmed Nawar
- ahmed sengab
- Ahmet Bakan
- Ahmet yldrm
- ailong
- Aishwarya Smriti
- Aiswarya
- Aiswarya Pawar
- Aitor Gonzalez
- aizoon_at_gmx.net
- Ajasja Ljubetič
- Re: any way to rotate and translate with mouse without changing modes? (Tue Jun 24 2014 - 15:37:39 CDT)
- Re: Scripting API: are arguments to representation types documented somewhere? (Mon Aug 20 2012 - 07:34:55 CDT)
- Re: VMD never finishes reading vis. state file, stalls and hoggs CPU (Fri Nov 25 2011 - 05:05:32 CST)
- Does this work with VMD: Nvidia 3DVision Glasses + SyncMaster 2233RZ + GTX 580 + Win7? (Sat Jul 09 2011 - 17:06:19 CDT)
- Re: VMD does not exit after running closest.tcl script in combination with bigdcd (Tue Jun 07 2011 - 09:02:10 CDT)
- Re: VMD does not exit after running closest.tcl script in combination with bigdcd (Tue Jun 07 2011 - 09:07:08 CDT)
- Re: trying to combine closewater.tcl with bigdcd.tcl error frame 3 out of range for molecule 0 (Wed May 25 2011 - 05:57:10 CDT)
- Re: trying to combine closewater.tcl with bigdcd.tcl error frame 3 out of range for molecule 0 (Tue May 24 2011 - 12:22:00 CDT)
- Re: trying to combine closewater.tcl with bigdcd.tcl error frame 3 out of range for molecule 0 (Tue May 24 2011 - 09:48:15 CDT)
- Re: PhD position in Computational Structural Biology at MPI Muenster (Fri May 13 2011 - 07:04:26 CDT)
- Ajasja Ljubeti
- Ajeeta kaushiki
- Ajith Gunaratne
- Ajith Rathnaweera Rajapaksha Mudalige
- Akash Banerjee
- Akash Mondal
- Akash Pandya
- Akemi Matsuno-Yagi
- Akemi Yagi
- Akif Ramzan
- Akiyama, Jotaro
- Akshata Rudrapatna
- Akshay Bhatnagar
- Akshay Patny
- Al Courey
- Al-Ali, Hassan
- Al-Rawi, Ahlam
- alamng_at_uci.edu
- Alan
- Alan Wilter Sousa da Silva
- alarcon_at_lncc.br
- Alba Colet Subirachs
- Albers, Thomas
- Albert
- albert albert
- Albert Solernou
- Albert Sun
- alberto
- alberto baldelli
- Alberto Perez
- Alberto Sergio Garay
- Alberto Torres
- aldo jongejan
- Ale Gomez
- Alec Robertson
- Alec Zander
- Alejandro Ortega
- Aleksander Debinski
- Aleksandr Kivenson
- Aleksei
- Aleksei Aksimentiev
- Alessandro Cembran
- Alessandro Mariani
- Alessandro Mascioni
- Alessandro Ruda
- Alessandro.Maiorana_at_roma2.infn.it
- Alessio Alexiadis
- Alex Angerhofer
- Alex Hahn
- Alex Hummels
- alex lin
- Alex Liu
- Alex Nazlidis
- Alex Peralvarez Marin
- Alex Richards
- Alex Saad-Falcon
- Alex Sha
- Alex Vakhrouchev
- Alexander A. Vakhrushev
- Alexander Adams
- Alexander Balaeff
- Alexander Beerhoff
- Re: can't build VMD on MacOs Ventura: use of undeclared identifier 'msms' (Tue Mar 07 2023 - 19:55:15 CST)
- can't build VMD on MacOs Ventura: use of undeclared identifier 'msms' (Tue Mar 07 2023 - 08:56:42 CST)
- Alexander Farley
- Alexander Howard
- Alexander Metz
- Alexander Peyser
- Alexander Spaar
- Alexandr Bezginov
- Alexandr Isayev
- Alexandr Kornev
- Alexandra Ringsby
- alexandra.marques_at_fc.up.pt
- Alexandre A. Vakhrouchev
- Alexandre Barrozo
- Alexandre PERRET
- Alexandre Suman de Araujo
- Re: Question about FFTK charge optimization procedure to CGENFF modeling (Tue May 14 2013 - 08:12:10 CDT)
- Question about FFTK charge optimization procedure to CGENFF modeling (Fri May 03 2013 - 15:40:41 CDT)
- Alexandre Suman de Araújo
- Alexandre Vakhrouchev
- Alexe Bojovschi
- Alexei Podtelezhnikov
- Alexei Rossokhin
- Alexey Kozlenkov
- Alexis Salas
- Alfred Shaohui Zheng
- Alfredo Quevedo
- Alfredo Valles
- Ali Ahmed
- Ali Alizadeh
- Re: Webinar on VMD's use of GPUs to accelerate MD visualization and analysis (Mon Feb 24 2014 - 10:07:36 CST)
- Ali Deyhim
- Ali Khanlarkhani
- Ali Morshedi
- Ali Osman Acar
- Ali Sheikholeslam
- Ali, Rejwan
- ali.kamrani91_at_REMOVE_yahoo.com
- Aliakbartehrani Zahra
- Aliasghar Alizadeh-Mojarad
- Alicia Hopkins
- Alilovic,Kata
- Alin Marin Elena - UKRI STFC
- Alin-Marin Elena - STFC UKRI
- Alisha \
- Alison Grinthal
- ALIYUN
- Allen, Caley R
- Re: FATAL ERROR: UNABLE TO FIND DIHEDRAL PARAMETERS FOR NH3 CT1 CT2A CT2 (ATOMS 1 5 7 10) (Mon Jan 27 2014 - 12:32:45 CST)
- Allison Rossetto
- Allison, Jane
- Almeida-Hernndez, Yasser, Dr.
- Almira Ovagimyan
- Althea Lake
- Alvea Tasneem
- Amadeu
- Amali Guruge
- Aman Jindal
- Amanda Jenkins
- Amarda Shehu
- Amaury Pupo Merio
- Amendra Fernando Hewa Dewage
- Ameya Harmalkar
- Amin Koochaki
- amin sagar
- amin_at_imtech.res.in
- Amir
- Amir Afshar
- Amir Hajiahmadi Farmahini
- Amir Hossein Saeedi Dehaghani
- Amir Suhail
- Amir Zeb
- Amira Yu
- amirhossein taghavi
- Amit
- amit dong
- Amit Gupta
- Amit Jaiswal
- amit kunte
- Amit Paliwal
- amit_at_mbu.iisc.ernet.in
- Amnah Alalmaie
- amodzelewska_at_dns.iimcb.gov.pl
- amodzelewska_at_iimcb.gov.pl
- Amor San Juan
- Amr Rizq
- Amrit Kalra
- Amy Rice
- Ana Celia Araujo Vila Verde
- script to load dcds from Replica Exchange simulations by Temperature (Mon Jan 15 2007 - 17:30:44 CST)
- RE: imposing period boundary conditions in a simulation with a crystal (Wed Sep 06 2006 - 08:31:59 CDT)
- the crystal structure of gold: questions about making the psf and about visualization in VMD; update (Tue May 23 2006 - 14:47:00 CDT)
- Ana Celia Vila Verde
- Ana Clia Vila Verde
- Ana Vila Verde
- Anand Kaushal
- Ananya Nayak
- Ananyo Bandyopadhyay
- anas forum
- Anatoliy
- Anatoly Chernyshev
- Anders Gabrielsson
- Andras Borosy
- andras.borosy_at_givaudan.com
- Andre Farias de Moura
- andre padilla
- andrea
- Andrea Bernini
- Andrea Carotti
- Andrea Cristiani
- Andrea Holfelder
- Andrea Kirkpatrick
- Andrea Spitaleri
- Re: Accessing tachyon optix from commandline and dat file generation (Tue Apr 04 2017 - 05:04:45 CDT)
- Re: Accessing tachyon optix from commandline and dat file generation (Mon Apr 03 2017 - 02:36:37 CDT)
- Andrea.Cristiani_at_pharm.unige.ch
- Andreas Kukol
- Andreas Tosstorff
- Andreas Wagenmann
- Andrei A Golosov
- Andrei Tudor
- Andrej Tekel
- Andres Bynum
- Andres Morales
- Andres Morales N
- Andres Palencia
- Andrew
- Andrew Dalke
- Re: What's the main reason of the structure or function of a protein? (Thu Mar 06 2008 - 00:25:03 CST)
- Andrew DeYoung
- Why are all carbon atoms lumped into C in the Name category in the colors dialog? (Fri Nov 29 2013 - 11:37:41 CST)
- Using Dipole Moment Watcher with Gromacs configurations and trajectories (Sat May 26 2012 - 12:20:09 CDT)
- Making only a subset of atoms transparent (or otherwise non-emphasized) (Tue May 15 2012 - 12:49:22 CDT)
- Andrew Doig
- Andrew Fenley
- Andrew Gormanly
- Andrew Hall
- Andrew Huang
- Andrew James Bennett
- Andrew Jewett
- Re: Feedback wanted from Linux VMD users with ATI/AMD graphics chipsets (Thu Nov 03 2011 - 15:56:37 CDT)
- Andrew M. Simms
- RE: mol urlload -- this doesn't seem to work in Windows (it does seem to work from Linux) (Fri Apr 16 2010 - 18:18:16 CDT)
- Andrew Petersen
- andrew ritchie
- Andrew Watts
- Andrew White
- Andrews, Casey
- Andrs Morales
- Re: Average angle between the lipid dipole vector and the bilayer normal. (Wed Apr 11 2012 - 16:43:01 CDT)
- Average angle between the lipid dipole vector and the bilayer normal. (Mon Apr 09 2012 - 12:55:17 CDT)
- Andy Lam
- Andy Liu
- aneamtu_at_iasi.mednet.ro
- aneesh cna
- angad sharma
- Angana Ray
- angel
- angel_at_cbuc.cl
- Angelo R. Rossi
- Angelo Rossi
- angelo vargas
- Anil Kumar
- Anirban Ghosh
- Anirudh Nandakumar
- Anjali Patel
- Anjela Manandhar
- AnkiReddy katha
- Re: fftk optimization of bonded parameters + Error: missing close-bracket (Thu Oct 31 2013 - 03:20:50 CDT)
- fftk optimization of bonded parameters + Error: missing close-bracket (Wed Oct 30 2013 - 03:08:57 CDT)
- Re: FFTK, pyrrolidine parametrization bonded parameters- issue with Hessian (Tue Oct 22 2013 - 06:59:59 CDT)
- ankit agrawal
- Anna
- Anna Aagaard
- Anna Amat
- Anna Battisti
- Anna Ceguerra
- Anna Karawajczyk
- Anna Kuznetsova
- Anna Lohning
- Anna Modzelewska
- Anna Petroff
- Anna Whitney
- Annabelle Posey
- annalisa_at_biotec.tu-dresden.de
- Anne Dara Bowen
- Anne Laustsen
- Anneta Tzampazi
- Annika Wittenbecher
- Anoop Krishnan
- anshudx_at_indiatimes.com
- Anshul Shah
- Anssi Nurminen
- Anthony Cruz
- Anthony Cruz Balberdi
- Anthony Cruz-Balberdy
- Anthony Ivetac
- Anthony Ma
- Anthony Rey
- Anthony Ruth
- Anthony Samiotakis
- Anton Arkhipov
- Re: Can the CG model built from VMD be used as an Input of NAMD,GROMACS and any other MD program? (Tue Apr 28 2009 - 10:34:04 CDT)
- Anton B. Guliaev
- Antonija Tomić
- Antonija Tomi
- Antonio Tilocca
- anu chandra
- anupama sharma
- Anuradha Mittal
- ANURAG JHA
- Anurag Sethi
- Anurag Sharma
- Anwaar Al-Zireeni
- anyy zsj
- apeyser_at_newssun.med.miami.edu
- aramice Malkhasian
- Arango, Andres Santiago
- Arash Azari
- Arash Firouzbakht
- aravind chandrasekaran
- Aravind Ravichandran
- Aravinda Munasinghe
- Araz Jakalian
- Archana Sonawani-Jagtap
- Ardavan Mehdizadeh
- Ardy Davari
- Aref Takiden
- Arent, Michael
- Arham Amouie
- Ari Turpeinen
- Arian Arian
- Aric Newton
- Arieana Moore
- Ariel Mitchell
- Arienti, Marco UTRC
- Arijit Ghosh
- Arindam Ganguly
- Aris Marcolongo
- Arjun Sharma
- Armando Jerome de Jesus
- Armen Nalian
- Arnab Chakrabarty
- Arnab Mukherjee
- Arneh Babakhani
- Re: Changing the Index values of a molecule (the differenece between gro and pdb files) (Wed Aug 15 2007 - 13:06:17 CDT)
- Changing the Index values of a molecule (the differenece between gro and pdb files) (Wed Aug 15 2007 - 12:39:08 CDT)
- Re: Using VMD just to plot some coordinates from a mathematical/geometrical model (Sat Jun 23 2007 - 10:29:11 CDT)
- Re: Using VMD just to plot some coordinates from a mathematical/geometrical model (Fri Jun 22 2007 - 20:04:40 CDT)
- Using VMD just to plot some coordinates from a mathematical/geometrical model (Fri Jun 22 2007 - 17:51:35 CDT)
- Re: Error while running scripts: terminate called after throwing an instance of 'std::bad_alloc' (Mon Feb 05 2007 - 10:59:04 CST)
- Re: Error while running scripts: terminate called after throwing an instance of 'std::bad_alloc' (Sun Feb 04 2007 - 21:58:19 CST)
- Re: Error while running scripts: terminate called after throwing an instance of 'std::bad_alloc' (Fri Feb 02 2007 - 20:04:29 CST)
- Arno Proeme
- Aronica, Pietro
- Arpita Srivastava
- Arsene Marian Alain
- Artem Mamonov
- Arthur Oliveira Vale
- Arthur Pereira da Fonseca
- Arthur Vale
- Artur Duque Rossi
- Artur Hermano
- Arturas
- Arturas Ziemys
- Arturo Fernandez
- Arun Krishnan
- arun kumar
- Arusha Acharyya
- Aryan Vahedi
- Aryan Vahedi-Faridi
- Asaf Farhi
- Asfa Ali
- Asghar Razavi
- Ash Johnson
- Ashar Malik
- Re: Creating PDB files of binding pockets that lists ligands first within the file (Tue Feb 02 2021 - 19:22:51 CST)
- Re: Questions about using VMD to modify/alter nucleic acid structures (Mon Sep 14 2020 - 03:48:25 CDT)
- Re: Create Binding Pocket of Every PDB File In A Directory Using TCL Scripts and Atomselect Command protein and within 4 of resname LIG (Mon Jul 20 2020 - 16:06:03 CDT)
- Re: Phi and Psi angles for particular residues as a function of time (Tue Jul 14 2020 - 11:27:50 CDT)
- Re: Using RMSD for individual residues script (as seen in the NAMD tutorial) and bigdcd (Mon Dec 09 2019 - 21:43:23 CST)
- Re: calculating number of water and osmolytes molecules at particular distance from protein surface. (Thu Jan 31 2019 - 00:00:10 CST)
- Re: Atomselection with the position selected conditions inside the loop is not working properly (Thu Aug 16 2018 - 11:22:21 CDT)
- Re: Atomselection with the position selected conditions inside the loop is not working properly (Thu Aug 16 2018 - 08:43:50 CDT)
- Re: Atomselection with the position selected conditions inside the loop is not working properly (Thu Aug 16 2018 - 06:50:38 CDT)
- Re: problem with mol IDs when running script from same VMD session. (Sun Jun 03 2018 - 14:29:11 CDT)
- Re: i thought I could run a 100 ns NAMD simulation in my laptop for a protein-hormone system containing around 2000 atoms in its pdb file(4lnx.pdb). But even to run a simulation for four hundred fifty thousand steps, it has taken almost 4700 minutes. is this normal or its low? the device has 4 cores with 16 gigs of ram and 4 gigs of gpu(amd). Or any suggestions to run it faster??? (Sun Mar 25 2018 - 20:44:48 CDT)
- Re: Decompose Transformation Matrix to Rotations and Translations along XYZ axes (Wed Mar 21 2018 - 13:29:17 CDT)
- Re: How to copy/paste a membrane patch to create a larger membrane? (Mon Feb 05 2018 - 10:14:19 CST)
- Re: Re: How can I measure bond length with “name ** and resid **" in scripts? (Tue Dec 19 2017 - 06:20:48 CST)
- Re: How can I measure bond length with “name ** and resid **" in scripts? (Tue Dec 19 2017 - 02:42:41 CST)
- Re: I would like to get a trajectory file in PDB. Can I use like data frame in VMD? (Wed Dec 13 2017 - 02:40:25 CST)
- Re: I would like to get a trajectory file in PDB. Can I use like data frame in VMD? (Wed Dec 13 2017 - 02:37:16 CST)
- Re: Moving atoms so that origin is at fixed position with respect to the display (Thu Oct 26 2017 - 14:41:59 CDT)
- Re: Finding atoms in protein-lipid system having electrostatic interaction (Wed Aug 09 2017 - 14:27:48 CDT)
- Re: solvate fails to set coordinates for the first few residues of the first chain? (Wed Apr 20 2016 - 00:29:41 CDT)
- Re: solvate fails to set coordinates for the first few residues of the first chain? (Tue Apr 19 2016 - 19:38:54 CDT)
- Re: solvate fails to set coordinates for the first few residues of the first chain? (Tue Apr 19 2016 - 19:33:32 CDT)
- Re: solvate fails to set coordinates for the first few residues of the first chain? (Tue Apr 19 2016 - 16:17:17 CDT)
- Re: Re: VMD Tricky selection of protein water bridge (2 bridge waters) (Fri Oct 02 2015 - 18:17:31 CDT)
- Re: How to extract data from NAMD log file for viscosity calculation (Tue Aug 18 2015 - 22:44:28 CDT)
- Re: How to continue the calculation of NAMD in case of power failure? (Sun May 17 2015 - 21:13:43 CDT)
- Re: Problem with generating psf and pdb files of metalloprotein made up of two fragments (Fri Mar 27 2015 - 06:11:27 CDT)
- Re: format I should use if I have different total number of atoms for each timesteps (Thu Dec 11 2014 - 20:58:14 CST)
- Re: A query about the deletion of Hydrogen and re-adding them by psfgen (Tue Dec 09 2014 - 19:44:20 CST)
- Re: A query about the deletion of Hydrogen and re-adding them by psfgen (Tue Dec 09 2014 - 16:50:08 CST)
- Fwd: How can I get the path of the TOP molecule in the tcl console? (Thu Dec 04 2014 - 22:15:51 CST)
- Re: Problem with merging structures!( psfgen) Warning: failed to set coordinate for atom AU0 AU:1 A) (Thu Nov 27 2014 - 08:48:56 CST)
- Re: Problem with merging structures!( psfgen) Warning: failed to set coordinate for atom AU0 AU:1 A) (Wed Nov 26 2014 - 17:02:34 CST)
- Ashish .Chauniyal
- ASHISH BIHANI
- Ashley Bennett
- Ashlynne Monroe
- Ashma Khan
- Ashraya Ravikumar
- asimplefunguy_at_netscape.net
- Asis Jana
- Asmaa Elsheshiny
- Assa Sittner
- Ata Madanchi
- Atanu Acharya
- Atanu Maity
- Athanassios Stavrakoudis
- Atila Iamarino
- Atila Petrosian
- rlwrap: Command not found. /usr/local/lib/vmd/vmd_LINUX: Command not found. (Fri Dec 09 2016 - 13:29:11 CST)
- Re: rlwrap: Command not found. /usr/local/lib/vmd/vmd_LINUX: Command not found. (Fri Dec 09 2016 - 01:55:18 CST)
- rlwrap: Command not found. /usr/local/lib/vmd/vmd_LINUX: Command not found. (Fri Dec 09 2016 - 01:49:42 CST)
- Atreya Dey
- Atreyo Pal
- Audrey Salazar
- Aurelie.DeLuca_at_sanofi-aventis.com
- Aurore Zyto
- Aurum Bai
- Austin Small
- AustinSmall_at_comcast.net
- Avell Diroll
- Avisek Das
- avl211_at_lehigh.edu
- Axel Berg
- Axel Kohlmeyer
- Re: Please help me understand the .dx file generated when using PME Electrostatics Analysis (Sat Dec 09 2023 - 14:48:21 CST)
- Re: Two questions: reordering molecule IDs and deleting frames with TCL commands (Sat Mar 11 2023 - 23:49:00 CST)
- Re: Two questions: reordering molecule IDs and deleting frames with TCL commands (Sat Mar 11 2023 - 23:23:27 CST)
- Re: Fwd: Problem building vmd with ospray - OSPRayRenderer.h error: ‘OSPModel’ does not name a typ (Thu Feb 23 2023 - 23:55:57 CST)
- Re: Problem with make_trajectory_movie_files script for lammps trajectory with -dispdev text (Fri Feb 17 2023 - 06:45:21 CST)
- Re: compiling VMD 1.9.3 under Ubuntu 22.04LTS: modern C library issues (Sat Jul 30 2022 - 16:04:14 CDT)
- Re: “Filesize limit exceeded (core dumped)Q=80=9D_with_VMD_on_Linux?= (Thu May 26 2022 - 12:09:10 CDT)
- Re: How to write a netcdf file in vmd from already loaded netcdf/dcd trajectory (Thu Dec 23 2021 - 06:16:31 CST)
- Re: Discrepancy in value of dihedral angles of a sugar molecule by VMD tools (Thu Jul 22 2021 - 07:41:39 CDT)
- Re: Compilation error: stride_LINUXAMD64', surf_LINUXAMD64, tachyon_LINUXAMD64 : No such file or directory (Thu Apr 22 2021 - 15:34:04 CDT)
- Re: BFEE plugin error: 'measure center: bad weight sum would cause divide by zero' (Thu Apr 22 2021 - 12:59:51 CDT)
- Re: Why do the coordinates of my atoms change when writing to a pdb file? (Sun Mar 21 2021 - 00:18:28 CDT)
- Re: OpenGL window not rendering over ssh but works when connecting from other computers and works fine locally (Thu Jan 21 2021 - 07:15:46 CST)
- Re: how to keep the bond , angle , dihedral and improper type after solvating the lammps data (Fri Jun 12 2020 - 15:04:44 CDT)
- Re: Is it possible to use VMD to plot RDFs where the cell volume/parameter changes at each time step? (Wed Oct 23 2019 - 15:49:48 CDT)
- Re: How to fix the position of the lipid bilayer in the trajectories (Wed Mar 13 2019 - 16:18:12 CDT)
- Re: Dipole Watcher Plugin - atom selection not updated at every frame when drawing dipoles (Mon Oct 22 2018 - 10:15:14 CDT)
- Re: Dipole Watcher Plugin - atom selection not updated at every frame when drawing dipoles (Thu Oct 18 2018 - 08:05:04 CDT)
- Re: Atomselection with the position selected conditions inside the loop is not working properly (Thu Aug 16 2018 - 08:14:03 CDT)
- Re: Building plugins with _USE_ZLIB (how to activate preprocessor macro) (Tue Mar 13 2018 - 16:53:08 CDT)
- Re: Building plugins with _USE_ZLIB (how to activate preprocessor macro) (Tue Mar 13 2018 - 16:32:37 CDT)
- Re: Building plugins with _USE_ZLIB (how to activate preprocessor macro) (Tue Mar 13 2018 - 16:30:12 CDT)
- Re: Atom type information is not incremented after merging two molecules. (Fri Feb 23 2018 - 04:02:27 CST)
- Re: Can specden produce the autocorrelation and not only the powerspectrum? (Tue Feb 06 2018 - 12:46:27 CST)
- Re: Topotools guessing angle and bond topology from CONNECT info in PDB files (Wed Nov 22 2017 - 13:25:20 CST)
- Re: Topotools guessing angle and bond topology from CONNECT info in PDB files (Wed Nov 22 2017 - 00:41:16 CST)
- Re: rlwrap: Command not found. /usr/local/lib/vmd/vmd_LINUX: Command not found. (Fri Dec 09 2016 - 13:51:56 CST)
- Re: rlwrap: Command not found. /usr/local/lib/vmd/vmd_LINUX: Command not found. (Fri Dec 09 2016 - 13:50:14 CST)
- Re: Distribute evenly n-molecules at m-angstroem from protein surface (Sun Dec 04 2016 - 00:29:54 CST)
- Re: selection atoms depending on bonding, selection of 'new' molecules (Fri Oct 14 2016 - 09:52:54 CDT)
- Re: by using Axel's HOOMD plugin, convert pdb to xml and missing bond information (Mon Sep 26 2016 - 06:11:58 CDT)
- Re: by using Axel's HOOMD plugin, convert pdb to xml and missing bond information (Sun Sep 25 2016 - 23:20:00 CDT)
- LAMMPS tutorial and Materials Simulation Symposium @ Temple, August 15-19, 2016 (Fri Apr 29 2016 - 21:11:16 CDT)
- Re: Problem wit solvating carbon nano-tube, psfgen) error reading atoms from psf file (Sun Feb 28 2016 - 11:48:58 CST)
- Re: What is the correct way of using "pbcwrap" with "atomselect [within]"? (Tue Feb 02 2016 - 02:07:21 CST)
- Re: OpenDX file format website down: What do the three values at each grid point represent (Mon Oct 05 2015 - 10:57:17 CDT)
- Re: OpenDX file format website down: What do the three values at each grid point represent (Fri Oct 02 2015 - 13:09:36 CDT)
- Re: Viewing gromacs .xtc trajectory 'Error reading timestep, file does not match format' (Thu Jun 25 2015 - 10:45:51 CDT)
- Re: Viewing gromacs .xtc trajectory 'Error reading timestep, file does not match format' (Thu Jun 25 2015 - 10:29:11 CDT)
- Re: Viewing gromacs .xtc trajectory 'Error reading timestep, file does not match format' (Thu Jun 25 2015 - 08:56:29 CDT)
- Re: Density Profile Tool: Is the selection updated as the frame is changed? (Wed May 27 2015 - 22:37:02 CDT)
- School on Molecular Dynamics and Enhanced Sampling Methods @ Temple University July 6-10, 2015 (Fri May 08 2015 - 11:29:01 CDT)
- Re: Fw: Colour coordinating atoms in a trajectory by Coordination Number (Mon Mar 30 2015 - 10:59:18 CDT)
- Re: Colour coordinating atoms in a trajectory by Coordination Number (Thu Mar 26 2015 - 12:08:48 CDT)
- GPU Programming workshop @ ICTP: deadline extended for participants not requiring visa and financial support (Tue Mar 24 2015 - 14:17:22 CDT)
- Re: Can I load NetCDF trajectories from AMBER in VMD on a Windows machine? (Sat Jan 17 2015 - 17:11:07 CST)
- Re: FFTK most probably doesn't work with molecules containing new atom types (Sat Dec 13 2014 - 18:15:42 CST)
- Re: FFTK most probably doesn't work with molecules containing new atom types (Sat Dec 13 2014 - 15:15:52 CST)
- Re: Problem with merging structures!( psfgen) Warning: failed to set coordinate for atom AU0 AU:1 A) (Thu Nov 27 2014 - 08:19:22 CST)
- Re: Problem with merging structures!( psfgen) Warning: failed to set coordinate for atom AU0 AU:1 A) (Wed Nov 26 2014 - 15:50:09 CST)
- Re: Problem with merging structures!( psfgen) Warning: failed to set coordinate for atom AU0 AU:1 A) (Wed Nov 26 2014 - 12:33:15 CST)
- Re: Problem with merging structures!( psfgen) Warning: failed to set coordinate for atom AU0 AU:1 A) (Wed Nov 26 2014 - 11:25:44 CST)
- Re: Problem with merging structures!( psfgen) Warning: failed to set coordinate for atom AU0 AU:1 A) (Wed Nov 26 2014 - 10:13:20 CST)
- Re: Fwd: namd-l: Why RDF increases as r increase instead of constant (Tue Nov 04 2014 - 14:29:41 CST)
- Re: Fwd: namd-l: Why RDF increases as r increase instead of constant (Tue Nov 04 2014 - 11:39:49 CST)
- Re: Fwd: namd-l: Why RDF increases as r increase instead of constant (Mon Nov 03 2014 - 15:49:48 CST)
- Re: Fwd: namd-l: Why RDF increases as r increase instead of constant (Mon Nov 03 2014 - 00:58:07 CST)
- Re: topotools question regarding ordering of bonds, angles, etc in output. (Fri Oct 03 2014 - 14:32:48 CDT)
- Re: topotools question regarding ordering of bonds, angles, etc in output. (Fri Oct 03 2014 - 13:16:37 CDT)
- Re: topotools question regarding ordering of bonds, angles, etc in output. (Fri Oct 03 2014 - 12:44:53 CDT)
- Re: create bonds with uniform pairwise cut off radius for XYZ trajectories. (Fri Sep 26 2014 - 06:47:40 CDT)
- Re: create bonds with uniform pairwise cut off radius for XYZ trajectories. (Fri Sep 26 2014 - 06:46:27 CDT)
- Re: create bonds with uniform pairwise cut off radius for XYZ trajectories. (Fri Sep 26 2014 - 03:59:32 CDT)
- Re: How to get all bond angles and bond distances for all atoms in sheet (Wed Sep 03 2014 - 10:30:27 CDT)
- Re: How to get all bond angles and bond distances for all atoms in sheet (Wed Sep 03 2014 - 10:17:38 CDT)
- Re: How to get all bond angles and bond distances for all atoms in sheet (Wed Sep 03 2014 - 03:07:04 CDT)
- Re: How to get all bond angles and bond distances for all atoms in sheet (Tue Sep 02 2014 - 08:37:31 CDT)
- Re: How to get all bond angles and bond distances for all atoms in sheet (Tue Sep 02 2014 - 08:42:38 CDT)
- Re: How to get all bond angles and bond distances for all atoms in sheet (Mon Sep 01 2014 - 08:19:05 CDT)
- Re: loading multiple trajectories with stride command in the terminal (Fri Jul 25 2014 - 10:42:57 CDT)
- School on Molecular Dynamics with NAMD and LAMMPS in Philadelphia, August 18-22 2014 (Thu Jul 17 2014 - 14:48:17 CDT)
- Re: convert AMBER format file to CHARMM format file or NAMD format file (Thu Apr 17 2014 - 11:03:49 CDT)
- Re: convert AMBER format file to CHARMM format file or NAMD format file (Wed Apr 16 2014 - 14:55:58 CDT)
- Re: Feature request: capturing tool location and steering forces in IMD trajectory (Mon Apr 07 2014 - 01:23:09 CDT)
- Re: problem for VMD extension_radial pair distribution function_truncation (Fri Mar 21 2014 - 11:08:28 CDT)
- Re: Why are all carbon atoms lumped into C in the Name category in the colors dialog? (Fri Nov 29 2013 - 19:13:50 CST)
- Re: Force field tool kit - missing close brackets-vmd version 1.9.2 (Mon Sep 30 2013 - 02:47:21 CDT)
- Re: Question regarding color schemes on crystals and grain boundaries (Sat Aug 31 2013 - 06:37:12 CDT)
- Re: Re: VRPN driver for Novint Falcon haptic device available - Looking for Testers (Sat Aug 17 2013 - 09:05:43 CDT)
- new VMD plugin for reading LAMMPS dumps with variable number of atoms (Thu Jul 25 2013 - 07:43:34 CDT)
- Re: Re: VRPN driver for Novint Falcon haptic device available - Looking for Testers (Wed Jul 03 2013 - 23:44:18 CDT)
- Re: how to calculate binding free energy and contribution of individual residue? (Mon Apr 22 2013 - 03:35:20 CDT)
- Re: put the water box in a grid and traverse for the atoms in each grid (Thu Apr 11 2013 - 03:20:26 CDT)
- Re: is there a way to measure the long axis of a protein or angle between domains in VMD (Wed Apr 10 2013 - 03:35:46 CDT)
- Re: Tethering, or restraining, part of a molecule during MD playback (Mon Mar 25 2013 - 01:42:46 CDT)
- Re: cp: cannot stat `../LINUXAMD64/vmd_LINUXAMD64': No such file or directory (Mon Mar 18 2013 - 11:00:26 CDT)
- Re: visualizing multiframe trajectory simultaneously with multimolecule (Mon Dec 17 2012 - 10:37:43 CST)
- Re: visualizing multiframe trajectory simultaneously with multimolecule (Sat Dec 15 2012 - 01:07:21 CST)
- Re: visualizing multiframe trajectory simultaneously with multimolecule (Thu Dec 13 2012 - 12:53:11 CST)
- Re: VMD 1.9.1 core dumps (CentOS-5 x86_64) nvidia drivers: 304.64/4x GTX 680 (Mon Dec 10 2012 - 10:22:49 CST)
- Re: Re: control the spacing between the dashes in the hydrogen bonding between two atoms (Tue Oct 30 2012 - 08:59:22 CDT)
- Re: Visualizing phonon displacement patterns from axsf format forces? (Sun Oct 21 2012 - 02:49:55 CDT)
- Re: coloring atoms based on max bond length; Need help with bond retrieval (Tue Oct 16 2012 - 10:33:57 CDT)
- Re: coloring atoms based on max bond length; Need help with bond retrieval (Mon Oct 15 2012 - 14:12:33 CDT)
- Re: VRPN driver for Novint Falcon haptic device available - Looking for Testers (Sun Oct 14 2012 - 13:31:12 CDT)
- Re: Possible handle leak in 'measure gofr' VMD 1.9.1 Windows (no cuda) (Sun Aug 26 2012 - 10:44:48 CDT)
- Re: Possible handle leak in 'measure gofr' VMD 1.9.1 Windows (no cuda) (Sun Aug 26 2012 - 08:05:00 CDT)
- Re: Scripting API: are arguments to representation types documented somewhere? (Mon Aug 20 2012 - 07:15:52 CDT)
- Re: connect a spring between all the atoms present in pdb structure (Sat Aug 04 2012 - 13:20:05 CDT)
- Re: namd-l: connect a spring between all the atoms present in pdb structure (Sat Aug 04 2012 - 13:21:27 CDT)
- anybody interested in running VMD in parallel (without recompiling)? (Wed May 30 2012 - 19:40:45 CDT)
- Re: Using Dipole Moment Watcher with Gromacs configurations and trajectories (Sat May 26 2012 - 16:19:26 CDT)
- Re: Making only a subset of atoms transparent (or otherwise non-emphasized) (Tue May 15 2012 - 13:38:17 CDT)
- Re: Is it possible to save the position and angle of the camera for future VMD sessions? (Fri Apr 13 2012 - 18:57:22 CDT)
- Re: Is there any way to stop the display of bonds for bonded atoms on opposite sides of a periodic boundary without unwrapping? (Fri Mar 30 2012 - 08:13:09 CDT)
- Re: information regarding tcl script for cell volume changing with each frame (Sat Mar 03 2012 - 17:25:43 CST)
- Re: information regarding tcl script for cell volume changing with each frame (Sat Mar 03 2012 - 14:45:14 CST)
- Re: How to change the python include and linkage path in configure script (Mon Feb 27 2012 - 13:33:18 CST)
- Re: [request] Best practices for rendering frames and making movies (Tue Feb 21 2012 - 18:29:19 CST)
- Re: Create multiple tcl interpreter child instances within VMD to run several scripts at once (Thu Feb 16 2012 - 12:46:48 CST)
- Re: Re: CUDA driver for Mac OS X 10.7 on Late 2008 13 inch Macbook with NVIDA GeForce 9400M 256 MB ? (Thu Jan 19 2012 - 13:55:04 CST)
- Re: Viewing System of Molecules where coordinates are in text file. (Thu Dec 01 2011 - 22:28:12 CST)
- Re: VMD never finishes reading vis. state file, stalls and hoggs CPU (Mon Nov 28 2011 - 10:21:20 CST)
- Re: VMD never finishes reading vis. state file, stalls and hoggs CPU (Fri Nov 25 2011 - 09:38:01 CST)
- Re: Use of RBCG to convert multiple frames from atomistic trajectory to Coarse grained (Tue Nov 01 2011 - 17:09:50 CDT)
- Re: coloring bonds on the same segments differently from those between segments (Thu Oct 20 2011 - 20:10:23 CDT)
- Re: How to select whole residues when at least one atom is within a specific distance (Thu Oct 13 2011 - 14:37:24 CDT)
- Re: Re: Selecting a laptop for VMD and NAMD (was: CUDA cores seen by VMD on GT540M) (Tue Sep 27 2011 - 10:36:20 CDT)
- Re: Showing and Calculating the amount of water molecules inside carbon nanotube (Tue Sep 13 2011 - 23:54:39 CDT)
- Re: define water cavity using atom selection in graphical representations window (Tue Sep 06 2011 - 09:28:45 CDT)
- Re: define water cavity using atom selection in graphical representations window (Tue Sep 06 2011 - 05:11:00 CDT)
- Re: define water cavity using atom selection in graphical representations window (Tue Sep 06 2011 - 05:31:23 CDT)
- Re: How can I draw secondary structures if I only have the carbon alpha coordinates (Thu Aug 18 2011 - 13:27:42 CDT)
- Re: how to draw different set of points for different frames in a trajectory my script does not work (Tue Jul 12 2011 - 15:17:50 CDT)
- Re: how to draw different set of points for different frames in a trajectory my script does not work (Fri Jul 08 2011 - 11:20:11 CDT)
- Re: how to draw different set of points for different frames in a trajectory my script does not work (Fri Jul 08 2011 - 08:31:17 CDT)
- Re: Re: best fit lines through two selections per each molecule ( I have 80 molecules) and the angle with another vector for each molecule (Tue Jun 28 2011 - 09:55:40 CDT)
- Re: trying to combine closewater.tcl with bigdcd.tcl error frame 3 out of range for molecule 0 (Wed May 25 2011 - 05:35:42 CDT)
- Re: trying to combine closewater.tcl with bigdcd.tcl error frame 3 out of range for molecule 0 (Tue May 24 2011 - 14:08:26 CDT)
- Re: trying to combine closewater.tcl with bigdcd.tcl error frame 3 out of range for molecule 0 (Tue May 24 2011 - 12:14:39 CDT)
- Re: vmd calculating wrong number of frames in xtc file using molinfo numframes ? (Mon May 23 2011 - 11:11:52 CDT)
- Re: Do psf generated by psfgen and psf produced by "$sel writepsf" function in VMD have different impact on MD simulation using NAMD? (Tue May 17 2011 - 09:44:26 CDT)
- Re: PhD position in Computational Structural Biology at MPI Muenster (Sun May 15 2011 - 16:47:40 CDT)
- Re: PhD position in Computational Structural Biology at MPI Muenster (Sun May 15 2011 - 11:51:22 CDT)
- Re: Questions about trajectory files obtained from LAMMPS Molecular dynamics with Reax Force field (Fri Apr 29 2011 - 08:36:01 CDT)
- Re: Linkage problem when compiling fortran bindings for VMD molfile plugins (Fri Mar 18 2011 - 11:14:31 CDT)
- Re: Linkage problem when compiling fortran bindings for VMD molfile plugins (Mon Mar 14 2011 - 18:08:53 CDT)
- Re: Linkage problem when compiling fortran bindings for VMD molfile plugins (Mon Mar 14 2011 - 13:43:28 CDT)
- Re: Dynamically updating water colors for each frame of a trajectory (Wed Feb 16 2011 - 18:01:35 CST)
- Re: VTF trajectory from coarse grained ESPReSo simulations. Visualization in Windows. (Wed Jan 12 2011 - 11:40:12 CST)
- Re: Volmap Tool: Angular or spatial correlation function around a center molecule (Thu Dec 30 2010 - 14:53:56 CST)
- Re: conversion of gromacs trajectory file (xtc) to amber trajectory file (mdcrd) (Sat Dec 25 2010 - 11:20:06 CST)
- Re: RE : Plot the value of the current frame in the Progress Bar for elapsed Time (Thu Dec 02 2010 - 13:44:37 CST)
- Re: Plot the value of the current frame in the Progress Bar for elapsed Time (Thu Dec 02 2010 - 10:47:31 CST)
- Re: protein breaks into parts after converting trajectory file to pdb file (Mon Sep 27 2010 - 10:32:58 CDT)
- Re: VMD questions about animating residue distance lines and contact maps (Fri Aug 13 2010 - 11:12:55 CDT)
- Re: Superimpose protein - plot water position - visualize water pathway (Sat Aug 07 2010 - 20:42:05 CDT)
- Re: PC suitable for visualisation of large systems, maximum namuber of atoms in a .pdb file (Wed Jul 21 2010 - 09:09:19 CDT)
- Re: PC suitable for visualisation of large systems, maximum namuber of atoms in a .pdb file (Wed Jul 21 2010 - 08:11:34 CDT)
- VRPN driver for Novint Falcon haptic device available - Looking for Testers (Fri Apr 23 2010 - 15:59:34 CDT)
- Re: vmd does not read pqr file correct, vmd parse chain information incorrect. (Tue Apr 20 2010 - 19:18:09 CDT)
- Re: problem with ied and vmd,ImportError: liblapack.so.3: cannot open shared object file: No such file or directory (Thu Mar 25 2010 - 10:49:09 CDT)
- Re: problem with ied and vmd,ImportError: liblapack.so.3: cannot open shared object file: No such file or directory (Thu Mar 25 2010 - 06:01:48 CDT)
- Re: bad text display in tk console (ubuntu 8.04 VMD 1.8.7 linux 32 bit) (Wed Jan 20 2010 - 11:42:57 CST)
- Re: bad text display in tk console (ubuntu 8.04 VMD 1.8.7 linux 32 bit) (Fri Jan 15 2010 - 12:11:21 CST)
- Re: aquire coordinates from the points of the solvent representation (Fri Nov 20 2009 - 13:23:11 CST)
- plugin for reading (and writing) trajectories with a varying number of atoms (Fri Nov 06 2009 - 14:51:02 CST)
- Re: namd-l: abnormal water surface after nvt and npt for POPC membrane (Wed Oct 28 2009 - 10:55:16 CDT)
- Re: Translating an atom along a specific direction and saving the pdb files (Tue Oct 20 2009 - 10:38:17 CDT)
- Re: X server is not capable of displaying double RGB images with a Z buffer (Tue Oct 20 2009 - 10:40:59 CDT)
- Re: Question about running tcl/tk script without graphic interface (vmd option -dispdev none ...) (Fri Oct 16 2009 - 18:25:07 CDT)
- Re: Why the win_version of vmd1.86 can not change to python interpreter? (Sat Aug 01 2009 - 09:30:12 CDT)
- Re: Problem: volumetric data coloring fails on AIX5_64 with GXT6500 OpenGL renderer (Thu Jul 23 2009 - 12:29:49 CDT)
- Re: Problem: volumetric data coloring fails on AIX5_64 with GXT6500 OpenGL renderer (Thu Jul 23 2009 - 11:23:34 CDT)
- Re: Problem: volumetric data coloring fails on AIX5_64 with GXT6500 OpenGL renderer (Mon Jul 20 2009 - 15:43:56 CDT)
- Re: Problem: volumetric data coloring fails on AIX5_64 with GXT6500 OpenGL renderer (Mon Jul 20 2009 - 11:36:28 CDT)
- Re: How to make a selection in atomselect using an element in a list? (Wed Jul 08 2009 - 11:17:14 CDT)
- GPGPU Programming summer school at University of Tennessee, Aug 10-14. (Mon Jun 29 2009 - 14:44:15 CDT)
- Re: "Re: ABINIT plugin ready for testing: can read GEO and DEN files. (Thu Jun 18 2009 - 11:13:59 CDT)
- Re: Re: ABINIT plugin ready for testing: can read GEO and DEN files. (Wed Jun 17 2009 - 12:01:30 CDT)
- Re: Re: ABINIT plugin ready for testing: can read GEO and DEN files. (Tue Jun 16 2009 - 22:59:20 CDT)
- Re: Re: ABINIT plugin ready for testing: can read GEO and DEN files. (Tue Jun 16 2009 - 07:31:03 CDT)
- Re: FW: Unable to render electrostatic potential cube files with most non-HF densities (Thu Jun 11 2009 - 09:19:21 CDT)
- bigdcd are related issues. was: Re: VMD 1.8.7 beta 3 posted for download... (Mon May 25 2009 - 11:42:59 CDT)
- Re: Plugin: molfile_plugin_t filename_extension; problem and bug... (Mon May 25 2009 - 09:52:04 CDT)
- Re: Sphere representaion with radius from pdb field "occupancy" or "temp. fac" (Wed May 13 2009 - 05:56:32 CDT)
- Re: Can the CG model built from VMD be used as an Input of NAMD,GROMACS and any other MD program? (Tue Apr 28 2009 - 08:32:24 CDT)
- Re: local packing density around a chemical group (say, a methyl group or a side chain) (Thu Apr 23 2009 - 11:27:20 CDT)
- Re: Can you show me an example of the .xyz file that is used to calculate the IR spectrum (Mon Feb 23 2009 - 14:46:18 CST)
- Re: passing arguments to a vmd script which is executed using play or source (Mon Feb 23 2009 - 10:20:55 CST)
- Re: passing arguments to a vmd script which is executed using play or source (Mon Feb 23 2009 - 09:15:44 CST)
- Re: passing arguments to a vmd script which is executed using play or source (Mon Feb 23 2009 - 09:08:58 CST)
- Re: error messages "*** glibc detected *** free(): invalid pointer" (Mon Feb 16 2009 - 12:26:19 CST)
- Re: how to set color parameters differently for different molecules (Thu Jan 29 2009 - 20:35:35 CST)
- Re: how to set color parameters differently for different molecules (Sun Jan 25 2009 - 13:18:10 CST)
- Re: accessing bonds angles dihedrals etc lists after PSF file is read into VMD (Fri Jan 23 2009 - 16:20:30 CST)
- Re: the exact definition of the keyword "radius" of the atom selection (Sat Dec 13 2008 - 16:37:11 CST)
- Re: [Fwd: problems with manipulating control switches on VMS main menu] (Fri Oct 31 2008 - 18:05:46 CDT)
- Re: why atomselection "protein" can not choose all the protein atoms with different alternate locations? (Mon Oct 13 2008 - 18:23:35 CDT)
- Re: trouble with running vmd after installation , machine gets hung (Sun Sep 21 2008 - 03:13:41 CDT)
- Re: trouble with running vmd after installation , machine gets hung (Fri Sep 19 2008 - 06:05:42 CDT)
- Re: problem controlling orientation of the simulation box drawn by pbctools (Sun Aug 10 2008 - 11:11:34 CDT)
- Re: Selecting atoms that have real SASA greater than 0, Not using "Surface" (Tue Jul 29 2008 - 20:40:30 CDT)
- Re: Mac OSX crash with bus error/segmentation fault upon loading pdb/dcd (Mon Jun 30 2008 - 13:17:20 CDT)
- Re: opening gromacs .gro file gives warning messsage and does not display the molecule (Tue Jun 17 2008 - 09:11:03 CDT)
- Re: measure hbonds between protein and water - problem with periodic boundary conditions (Thu Apr 17 2008 - 04:52:29 CDT)
- Re: compilation with python 2.5 and file permissions from the CVS repository (Mon Apr 14 2008 - 05:16:19 CDT)
- RE: compilation with python 2.5 and file permissions from the CVS repository (Sun Apr 13 2008 - 15:00:12 CDT)
- Re: compilation with python 2.5 and file permissions from the CVS repository (Sun Apr 13 2008 - 12:58:26 CDT)
- Re: Can VMD show the interactions between different structure part? (Thu Mar 27 2008 - 06:43:41 CDT)
- Re: Can VMD show the interactions between different structure part? (Wed Mar 26 2008 - 23:19:40 CDT)
- Re: unusual bond between the cysteine and arginine residue during the simulation (Fri Feb 29 2008 - 13:47:55 CST)
- Re: how to load a molecule in pdb format and save in mol2 format in batch mode (Mon Jan 14 2008 - 03:39:58 CST)
- Re: How to choose part of the volume data for isosurface visualization? (Tue Jan 08 2008 - 11:37:29 CST)
- Re: Selecting water molecules within 5 ang in a trajectory( generated by amber). (Wed Dec 26 2007 - 14:12:05 CST)
- Re: Trying to get VMD to run locally while logged into a remote machine (Wed Nov 21 2007 - 16:35:50 CST)
- Re: gui RMSD vs text RMSD calcs differ b/c ddiff backbone atom definitions (Sat Nov 17 2007 - 00:11:54 CST)
- Re: installed vmd_LINUXIA64 but recieve error : /usr/local/vmd/vmd_LINUX: command not found (Wed Nov 14 2007 - 20:34:06 CST)
- Re: installed vmd_LINUXIA64 but recieve error : /usr/local/vmd/vmd_LINUX: command not found (Tue Nov 13 2007 - 23:50:04 CST)
- Re: problem with colouring the surface with electroststic potential (Tue Nov 13 2007 - 02:15:54 CST)
- behavior of "mol addfile first/last" with non-integer frame numbers (Thu Sep 27 2007 - 19:35:40 CDT)
- Re: change the representation of certain atoms which pass a geometric criterion during a movie (Tue Sep 18 2007 - 08:34:29 CDT)
- Re: the console window is automatically closed without any error messages (Thu Sep 06 2007 - 12:50:08 CDT)
- Re: Changing the Index values of a molecule (the differenece between gro and pdb files) (Wed Aug 15 2007 - 12:51:30 CDT)
- Re: Very peculiar problem with bigdcd if not running interactively (post moved over from namd forum) (Wed Aug 15 2007 - 10:47:46 CDT)
- Re: how to make user input during runtime of a tcl program using TkConsole? (Fri Aug 10 2007 - 10:20:47 CDT)
- Re: Loading files into already-running version of VMD from command prompt (Sat Aug 04 2007 - 16:04:31 CDT)
- Re: orientation of hexahedrons parallelepipeds unit cells relative to x,y axes (Sat Jul 28 2007 - 17:24:08 CDT)
- Re: frame number input in tcl and direct mol graph display update (II) (Fri Jul 27 2007 - 13:56:05 CDT)
- Re: nonstandard solvate + cyclic peptides in explicit DMSO box + gofr (Thu Jul 26 2007 - 11:48:08 CDT)
- Re: Using VMD just to plot some coordinates from a mathematical/geometrical model (Sat Jun 23 2007 - 09:23:20 CDT)
- Re: lipid Scd order parameter for a large bilayer (1440 lipids) with a changing bilayer normal (ie. bilayer undulations) (Wed May 30 2007 - 14:14:08 CDT)
- Re: problem using bigdcd.tcl script does not run beyond the first frame no error reported (Mon May 07 2007 - 08:36:50 CDT)
- Re: RE: "which files to make a spatial grid?" => Bug for list command? (Tue Apr 17 2007 - 07:25:11 CDT)
- Re: problem using NAMD trajectory in charmm 32-bit, 64-bit etc. (yes, I posted this on charmm lists too) (Tue Apr 03 2007 - 09:20:25 CDT)
- Re: VMD-1.8.5: GLSL & NVidia troubles + fixed previous Spaceball problem (Sun Feb 11 2007 - 12:51:06 CST)
- Re: Saving mutli-molecule structures in VMD (e.g., for building membranes) (Mon Feb 05 2007 - 12:09:15 CST)
- Re: Error while running scripts: terminate called after throwing an instance of 'std::bad_alloc' (Sat Feb 03 2007 - 06:31:49 CST)
- Re: Compute the angle between a vector and the largest inertia axis (Tue Jan 30 2007 - 11:16:32 CST)
- Re: VMD 1.8.5 installed. The graphics flashed and disappeared after installation. (Tue Dec 19 2006 - 14:15:00 CST)
- Re: imposing period boundary conditions in a simulation with a crystal (Wed Sep 06 2006 - 09:23:39 CDT)
- Re: imposing period boundary conditions in a simulation with a crystal (Tue Sep 05 2006 - 12:00:19 CDT)
- Re: VMD crashed due to: vmd_LINUXAMD64: indirect_vertex_array.c:659: emit_DrawArrays_old: Assertion `elements_per_request >= count' failed (Tue Jun 27 2006 - 22:17:01 CDT)
- Re: VMD crashed due to: vmd_LINUXAMD64: indirect_vertex_array.c:659: emit_DrawArrays_old: Assertion `elements_per_request >= count' failed (Tue Jun 27 2006 - 19:53:00 CDT)
- Re: How to select water near a certain residue if it is outside of the water box? (Sat May 13 2006 - 18:11:27 CDT)
- Re: VMD-L: how to select water molecules between two residues in a trajectory. (Mon Apr 17 2006 - 11:33:38 CDT)
- Re: VMD-L: how to select water molecules between two residues in a trajectory. (Mon Apr 17 2006 - 10:50:38 CDT)
- Re: VMD-L: how to select water molecules between two residues in a trajectory. (Sat Apr 15 2006 - 20:31:11 CDT)
- Re: using gimp for converting jpg, tga ... images to high quality eps files (Mon Feb 07 2005 - 06:31:44 CST)
- Re: using gimp for converting jpg, tga ... images to high quality eps files (Sat Feb 05 2005 - 04:58:35 CST)
- Re: Re: vmd not starting up on Fedora core 3 linux , nVidia quadro 980 XGL, nVidia 6629 driver (Tue Jan 11 2005 - 10:50:57 CST)
- Re: vmd not starting up on Fedora core 3 linux , nVidia quadro 980 XGL, nVidia 6629 driver (Fri Jan 07 2005 - 07:20:17 CST)
- Re: vmd not starting up on Fedora core 3 linux , nVidia quadro 980 XGL, nVidia 6629 driver (Fri Jan 07 2005 - 06:37:21 CST)
- Re: vmd not starting up on Fedora core 3 linux , nVidia quadro 980 XGL, nVidia 6629 driver (Fri Jan 07 2005 - 05:40:13 CST)
- AYTUG TUNCEL
- Ayşe Özlem Aykut
- Aye zlem Sezerman
- Aziz, John
- B
- B $B6Q
- B. Bennion
- B.D Allen
- B.M.B. Vanschouwen
- Babban Mia
- Bachir Aoun
- Badmos, Sakiru
- Bahaa Mostafa
- Bailey, Steven
- Bakary N'tji Diallo
- Baker, Joseph
- Bala subramanian
- balas002_at_bama.ua.edu
- Balazs Jojart
- BALCZIAK, LOUIS
- Balu, Radhakrishnan (Cont, ARL/WMRD)
- Bamidele Adisa
- Ban Arn
- BAN,YOUNG MIN
- Bankf of the West
- Baofu Qiao
- baogen duan
- Baoqiang Cao
- Barbault Florent
- barrett
- Barry Bickmore
- Barry Isralewitz
- Re: what's the Letter in figure caption meaning of TIME-LINE 2nd structure present? (Mon May 07 2012 - 12:32:42 CDT)
- Re: Visualizing Timeline (tml) data w/o having to load trajectories (Thu Oct 27 2011 - 13:25:08 CDT)
- Bart Bruininks
- Re: VRAM memory piling up OPTIX 1.9.4a42 rendering consecutive frames (Tue Jun 16 2020 - 07:29:14 CDT)
- Re: VRAM memory piling up OPTIX 1.9.4a42 rendering consecutive frames (Wed Jun 10 2020 - 11:07:58 CDT)
- Re: VRAM memory piling up OPTIX 1.9.4a42 rendering consecutive frames (Wed Jun 10 2020 - 08:37:09 CDT)
- Re: Loading large trajectories using multiple threads/direct calls? (Thu Dec 05 2019 - 17:06:26 CST)
- Bartek Dobrzelecki
- Basak Isin
- Basanta Acharya
- Basheer Subei
- Bashir
- Bashir Fotouhi
- Bassam Haddad
- Re: Create Binding Pocket of Every PDB File In A Directory Using TCL Scripts and Atomselect Command protein and within 4 of resname LIG (Mon Jul 20 2020 - 13:31:24 CDT)
- Re: Create Binding Pocket of Every PDB File In A Directory Using TCL Scripts and Atomselect Command protein and within 4 of resname LIG (Mon Jul 20 2020 - 12:58:36 CDT)
- Re: analyzing amino acids forming pore constrictions in a channel protein (Tue Jun 02 2020 - 12:33:03 CDT)
- Baumert, Uwe Dr.rer.nat.
- baxy
- bbickmore_at_comcast.net
- Beat Meier
- Behnam Ghalami
- Behrmann, Elmar
- Ben Chern
- Re: Can VMD show the interactions between different structure part? (Thu Mar 27 2008 - 20:26:13 CDT)
- Ben Cornett
- Ben Cossins
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- Benjamin Kaduk
- Benjamin SCHWARZ
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- Benjamin.Haberl_at_physik.uni-muenchen.de
- Bennion, Brian
- RE: how to explore the frame number in clustering analysis by the clustering plugin (Thu Jul 07 2016 - 16:05:37 CDT)
- RE: a script to count the frames in which some water molecules interact with selected protein atoms (Tue Dec 30 2014 - 10:25:41 CST)
- RE: how to convert dcd AND ALIGN molecules then to pdbs in command line (Thu Apr 11 2013 - 10:08:08 CDT)
- RE: how to convert dcd AND ALIGN molecules then to pdbs in command line (Wed Apr 10 2013 - 11:52:03 CDT)
- RE: visualizing multiframe trajectory simultaneously with multimolecule (Mon Dec 17 2012 - 10:19:02 CST)
- RE: visualizing multiframe trajectory simultaneously with multimolecule (Fri Dec 14 2012 - 17:06:03 CST)
- visualizing multiframe trajectory simultaneously with multimolecule (Thu Dec 13 2012 - 11:46:18 CST)
- RE: VMD can't display new PDB secondary structure properly (pyMol, jMol can) (Mon Nov 19 2012 - 17:30:19 CST)
- BERGY
- Berit Hinnemann
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- Re: Ignore all the errors and load severely wrong structure in XYZ format (Sat Jun 10 2017 - 16:07:40 CDT)
- Bharath K. Srikanth
- Bhargava
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- Bian Li
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- bizoniusz_at_o2.pl
- Bjoern Olausson
- Re: VMD never finishes reading vis. state file, stalls and hoggs CPU (Wed Nov 30 2011 - 10:11:53 CST)
- Re: VMD never finishes reading vis. state file, stalls and hoggs CPU (Mon Nov 28 2011 - 02:54:17 CST)
- Re: VMD never finishes reading vis. state file, stalls and hoggs CPU (Fri Nov 25 2011 - 05:36:26 CST)
- Bjoern Windshuegel
- Björn Forsberg
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- Bjrnar Jensen
- Blake Charlebois
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- Re: Problems with licorice representation when rendering 3D PDF for Power Point (Fri Apr 23 2010 - 09:59:08 CDT)
- Problems with licorice representation when rendering 3D PDF for Power Point (Thu Apr 22 2010 - 14:56:52 CDT)
- Bob Milius
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- Re: Slow display with nVidia GeForce 9400GT and 3xx drivers on Linux (Mon Apr 15 2013 - 05:51:10 CDT)
- Re: Slow display with nVidia GeForce 9400GT and 3xx drivers on Linux (Mon Mar 18 2013 - 07:19:09 CDT)
- Re: Slow display with nVidia GeForce 9400GT and 3xx drivers on Linux (Fri Mar 08 2013 - 11:56:12 CST)
- Re: Re: VMD 1.9.1 core dumps (CentOS-5 x86_64) nvidia drivers: 304.64/4x GTX 680 (Tue Dec 11 2012 - 07:50:23 CST)
- Re: vmd not starting up on Fedora core 3 linux , nVidia quadro 980 XGL, nVidia 6629 driver (Tue Jan 11 2005 - 10:42:25 CST)
- Bogdan Tarus
- Bokas George
- Bonakala Satyanarayana
- bond.james
- Bongkeun Kim
- bonicoli_at_loria.fr
- bora erdemli
- Boris Steipe
- Re: VMD can't display new PDB secondary structure properly ( pyMol, jMol can). . (Tue Nov 20 2012 - 14:44:53 CST)
- Borne, Vincent
- Bose, Ritwika
- Boshra Moradi
- bozell, joe
- brad noyes
- Bram Stolk
- Brandon Havranek
- Branko