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NAMD-L: By messages with attachments

By messages with attachments

2670 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive

Starting: Fri Jan 02 2015 - 23:19:01 CST
Ending: Tue Dec 27 2016 - 20:48:03 CST

• NAMD_2.12b1 build on Cray XC40 is failing Ianni, James C CTR USARMY RDECOM ARL (US) (Mon Dec 12 2016 - 14:35:32 CST)
  1. smime.p7s (5430 bytes)
• Minimization error Santanu Santra (Tue Dec 06 2016 - 23:00:04 CST)
  1. xxxxx.conf (1953 bytes)
• How to create 3'-3' phosphodiester linkage for a DNA. Susmita Ghosh (Mon Nov 28 2016 - 23:50:26 CST)
  1. image.png (20003 bytes)
• Re: A common tool to read the output of NAMD run Ajasja Ljubetič (Mon Nov 28 2016 - 08:34:47 CST)
  1. to-ener.py (1242 bytes)
• REMD kaushik chakraborty (Wed Nov 23 2016 - 13:58:51 CST)
  1. ubq_ww_pcv1.conf (1135 bytes)
  2. replica.conf (593 bytes)
• Re: Generate psf file in x-plor format Nehad Elsalamouny (Thu Nov 17 2016 - 14:44:40 CST)
  1. xxxx.psf (24093 bytes)
  2. ATT00001.htm (2591 bytes)
• RE: visualizing and analyzing long simulation Deng, Jinxia (Nancy) (Mon Oct 10 2016 - 10:51:42 CDT)
  1. image001.png (25350 bytes)
• Re: question regarding rmsd Leandro Martínez (Wed Oct 05 2016 - 15:58:39 CDT)
  1. rmsd.png (13568 bytes)
• RE: question regarding rmsd Radak, Brian K (Wed Oct 05 2016 - 15:39:01 CDT)
  1. rmsd.png (13568 bytes)
• Re: question regarding rmsd Dhiraj Srivastava (Wed Oct 05 2016 - 14:02:32 CDT)
  1. rmsd.png (13568 bytes)
• Re: question regarding rmsd Pardis Tabaee (Wed Oct 05 2016 - 13:34:41 CDT)
  1. rmsd.png (13568 bytes)
• RE: question regarding rmsd Radak, Brian K (Wed Oct 05 2016 - 11:18:12 CDT)
  1. rmsd.png (13568 bytes)
• Re: question regarding rmsd Roshan Shrestha (Wed Oct 05 2016 - 11:07:09 CDT)
  1. rmsd.png (13568 bytes)
• Re: question regarding rmsd Pardis Tabaee (Wed Oct 05 2016 - 10:55:01 CDT)
  1. rmsd.png (13568 bytes)
• question regarding rmsd Dhiraj Srivastava (Tue Oct 04 2016 - 16:07:43 CDT)
  1. rmsd.png (13568 bytes)
• convert .xyz file in .psf file for non-protein molecule grenier_at_cinam.univ-mrs.fr (Thu Sep 08 2016 - 10:20:03 CDT)
  1. azacalix.xyz (3360 bytes)
• PMF Calculation Crystal Liu (Fri Aug 12 2016 - 19:15:46 CDT)
  1. 08-12_at_2.14.31_PM.png (7861 bytes)
  2. 08-12_at_3.37.50_PM.png (27699 bytes)
• namd2 seg fault NAMD_2.11_Source Linux-x86_64-g++ Doug Stetner (Tue Jul 12 2016 - 22:51:40 CDT)
  1. signature.asc (843 bytes)
• Regarding radial distribution function graph siddharth kamal (Thu Jun 16 2016 - 08:31:23 CDT)
  1. O.eps (21785 bytes)
• Colvars: Unable to restrict rotation and translation along y and z axes Sourav Ray (Wed May 18 2016 - 07:22:00 CDT)
  1. ref.pdb (57587 bytes)
• ffTK fitting dihedrals Seth Axen (Tue May 17 2016 - 01:36:02 CDT)
  1. multiplot.png (25517 bytes)
• Re: Srijita Paul (Tue May 10 2016 - 08:41:10 CDT)
  1. nvt.namd (2960 bytes)
  2. npt_eq.namd (3306 bytes)
• (no subject) Srijita Paul (Sat Apr 16 2016 - 00:06:47 CDT)
  1. top_urea.rtf (889 bytes)
• Re: AW: problem with +devices using nikolaev_at_spbau.ru (Tue Apr 05 2016 - 07:41:17 CDT)
  1. CPUINFO (46690 bytes)
• Re: Running multi-node jobs on Sun Grid Engine Sourav Ray (Tue Apr 05 2016 - 00:19:23 CDT)
  1. Sun_Grid_Engine.sh (470 bytes)
• Running multi-node jobs on Sun Grid Engine Sourav Ray (Sun Apr 03 2016 - 10:49:30 CDT)
  1. _single_node.sh (469 bytes)
  2. PBS.sh (1324 bytes)
  3. Other.sh (840 bytes)
• Occasional performance slow down using NAMD with Xeon Phi Mattia Felice Palermo (Fri Apr 01 2016 - 09:53:37 CDT)
  1. avg_load.pdf (6988 bytes)
  2. max_load.pdf (7584 bytes)
• NAMD 2.11 CUDA freezes on windows 8 Ajasja Ljubetič (Wed Mar 16 2016 - 13:08:59 CDT)
  1. COMPUTER-A-NAMD.2.10-CUDA-WORKS.txt (11196 bytes)
  2. COMPUTER-A-NAMD.2.11-WORKS.txt (9424 bytes)
  3. COMPUTER-A-NAMD.2.11-CUDA-NOT_WORKING.txt (10608 bytes)
• WG: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800 Greipel.Joachim_at_mh-hannover.de (Mon Mar 14 2016 - 04:47:28 CDT)
  1. smime.p7s (5649 bytes)
• Fwd: ISQBP 2016 meeting - registration opened! Vlad Cojocaru (Mon Mar 14 2016 - 03:13:10 CDT)
  1. Attached_Message_Part (135 bytes)
• AW: vmd-l: NAMD 2.11 Cuda does not work with Quadro FX 3800 Greipel.Joachim_at_mh-hannover.de (Fri Mar 11 2016 - 01:47:27 CST)
  1. smime.p7s (5649 bytes)
• Energy gradient in colvars.state file Carlo Guardiani (Mon Feb 29 2016 - 13:09:31 CST)
  1. Energy_Gradients.agr (17708 bytes)
• Re: Replica Exchange US, Colvar suggestion Abhishek TYAGI (Sat Feb 13 2016 - 22:39:29 CST)
  1. _amp__X1f610.png (459 bytes)
• Replica Exchange US, Colvar suggestion Abhishek TYAGI (Sat Feb 13 2016 - 01:07:38 CST)
  1. 1.conf (16132 bytes)
  2. colvars.conf (309 bytes)
• bond energy high Ipsita Basu (Wed Feb 03 2016 - 05:15:35 CST)
  1. file (4177 bytes)
• RE: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Downs, Andrew S CTR USARMY ARL (US) (Tue Jan 12 2016 - 14:04:36 CST)
  1. winmail.dat (8793 bytes)
• RE: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Downs, Andrew S CTR USARMY ARL (US) (Tue Jan 12 2016 - 09:44:54 CST)
  1. winmail.dat (8009 bytes)
• RE: [Non-DoD Source] AW: Compilation error across Intel 14, 15 and 16 (UNCLASSIFIED) Downs, Andrew S CTR USARMY ARL (US) (Tue Jan 12 2016 - 07:27:59 CST)
  1. winmail.dat (7333 bytes)
• Re: Regarding system forces in NAMD sruthi c k (Fri Jan 08 2016 - 06:14:08 CST)
  1. Histogram.eps (20972 bytes)
  2. Av_system_force.eps (21181 bytes)
• Fwd: Regarding system forces in NAMD sruthi c k (Fri Jan 08 2016 - 03:38:26 CST)
  1. Histogram.eps (20972 bytes)
  2. Av_system_force.eps (21181 bytes)
• DIDN'T FIND vdW PARAMETER FOR ATOM TYPE SG3O1 Srijita Paul (Fri Dec 25 2015 - 00:41:47 CST)
  1. o-sulfate.params (2328 bytes)
• (no subject) Srijita Paul (Tue Dec 22 2015 - 00:06:49 CST)
  1. o-sulfate.pdb (1616 bytes)
• Re:Re: Determining the PMF with Adaptive Biasing Forces sunyzero (Tue Dec 08 2015 - 22:00:19 CST)
  1. Q_88_AA_E5_9B_BE1.png__ (18294 bytes)
• buffer overflow with long file paths in psfgen in NAMD 2.11b2? Brian Radak (Tue Dec 08 2015 - 15:54:28 CST)
  1. PSFGEN_BUFFER_BUG.tgz (17025 bytes)
• Re: Determining the PMF with Adaptive Biasing Forces Jérôme Hénin (Tue Dec 08 2015 - 09:09:58 CST)
  1. ______1.png (18294 bytes)
• Re: Determining the PMF with Adaptive Biasing Forces Souvik Sinha (Tue Dec 08 2015 - 01:42:34 CST)
  1. ______1.png (18294 bytes)
• Determining the PMF with Adaptive Biasing Forces sunyzero (Mon Dec 07 2015 - 23:48:55 CST)
  1. Q_88_AA_E5_9B_BE1.png__ (18294 bytes)
• modify input file for production phase MD Deng, Jinxia (Nancy) (Fri Dec 04 2015 - 11:31:26 CST)
  1. step7.1_production.inp (7636 bytes)
• error when use Charmm_Gui prepared *.inp for NAMD Deng, Jinxia (Nancy) (Thu Dec 03 2015 - 08:37:14 CST)
  1. step6.1_equilibration.inp (4678 bytes)
• Fw: vmd-l: what is difference between "TOTAL", “TOTAL2" and "POTENTIAL" in the VMD plugin NAMD Plot? 孙业平 (Mon Nov 09 2015 - 06:49:42 CST)
  1. pawel_kedzierski.vcf (581 bytes)
• Weird psfgen bug? Tristan Croll (Fri Oct 30 2015 - 03:22:06 CDT)
  1. 2ma.str (7417 bytes)
  2. 2MA_ideal.pdb (3988 bytes)
  3. 2MA_ideal_autopsf.pdb (2815 bytes)
  4. 2MA_ideal_autopsf.psf (10710 bytes)
• Biasing potential of a Metadynamics Simulation Fidan Sumbul (Tue Oct 27 2015 - 13:05:02 CDT)
  1. 4AKE_r2b2_temp.restart.colvars.state (2884 bytes)
  2. 4AKE_r2b2_temp.colvars.traj (1237 bytes)
• Dielectric constant of water from MSM and PME simulations Mattia Felice Palermo (Fri Oct 23 2015 - 08:57:37 CDT)
  1. gr_OO.pdf (6572 bytes)
• AW: Compilation of NAMD from Source (Cray XC40) Richter, Stefan (Tue Oct 13 2015 - 13:10:44 CDT)
  1. NAMD_2.10.compilation.log (30696 bytes)
• Regarding problem in psfgen of heparin siddharth kamal (Fri Oct 02 2015 - 14:20:15 CDT)
  1. vmdscene3.jpg (29024 bytes)
• Re: Adaptive tempering implementation in NAMD differs Sachin Natesh (Thu Sep 24 2015 - 20:28:36 CDT)
  1. tempvtime_sim2_ubq.png (50605 bytes)
• Re: string method in NAMD 2.10 Chris Chipot (Tue Sep 22 2015 - 10:46:28 CDT)
  1. swarms.namd (9867 bytes)
• Re: node file for NAMD Sourav Ray (Sat Sep 12 2015 - 01:11:30 CDT)
  1. NAMDScript.txt (1398 bytes)
• parameters problem in sulfated molecules Lara rajam (Tue Sep 01 2015 - 12:12:42 CDT)
  1. 08-29_at_9.51.39_AM.png (18277 bytes)
• heparin Lara rajam (Sat Aug 29 2015 - 18:48:08 CDT)
  1. 08-29_at_9.51.39_AM.png (18277 bytes)
• PME Seg Fault Richard Overstreet (Mon Aug 10 2015 - 09:11:27 CDT)
  1. pore_5_2__i.conf (3817 bytes)
• The 2 NAMD tests "Alanin" and "tclforces" fail to run with "Atoms moving too fast" error Sriram Adhyapak (Mon Jul 27 2015 - 20:36:14 CDT)
  1. AtomTooFastTests.tar.gz (15301 bytes)
• NAMD hybrid configuration: Atoms moving too fast error Puneet Singh (Mon Jul 27 2015 - 06:41:38 CDT)
  1. namd_with_smpError.log (8662 bytes)
  2. namd_with_nonsmpError.log (911 bytes)
  3. namd_with_nonsmp.log (9612 bytes)
  4. namd_build_smp.sh (8829 bytes)
  5. namd_build.sh (8812 bytes)
• segmentation fault when running with mpirun Puneet Singh (Fri Jul 24 2015 - 08:05:23 CDT)
  1. namd_build.sh (7012 bytes)
• RE: Create psf file Raed Ahmed Abdelsalam Shalaby (Mon Jun 22 2015 - 05:54:32 CDT)
  1. ligand_top (2650 bytes)
• Create psf file Fransiska Kurniawan (Sat Jun 20 2015 - 17:56:52 CDT)
  1. tartrazine.pdb (6298 bytes)
  2. toppar_tartrazine.txt (7892 bytes)
• Different trajectories with and without restarting Grzegorz Nawrocki (Fri May 15 2015 - 18:09:57 CDT)
  1. input.tar.gz (3037 bytes)
• Re: performance question Thomas C. Bishop (Tue Apr 28 2015 - 14:32:16 CDT)
  1. benchmarks.v3.pdf (62457 bytes)
• Re: Re: Problems to parametrize molecules Evandro Semighini (Fri Apr 24 2015 - 13:58:25 CDT)
  1. b_list.str (6732 bytes)
• Problems when running FEP for mutation ASP to GLY Yunhui Peng (Fri Apr 17 2015 - 13:53:03 CDT)
  1. script.namd (2877 bytes)
• Re: problem restarting multiple walker metadynamics Amy Rice (Thu Apr 02 2015 - 14:54:56 CDT)
  1. meta_test_output.zip (17586 bytes)
  2. KR12_test.zip (7651 bytes)
• Re: problem restarting multiple walker metadynamics Giacomo Fiorin (Wed Apr 01 2015 - 15:05:30 CDT)
  1. multiple_walker_meta.zip (37080 bytes)
• Re: NAMD Subbarao Kanchi (Tue Mar 24 2015 - 01:48:39 CDT)
  1. implicit.conf (3941 bytes)
• Truncated octahedron : Problems in PBC when reading a dcd file with NAMD Panel Nicolas (M.) (Mon Mar 16 2015 - 11:18:00 CDT)
  1. postX.inp (3876 bytes)
• FATAL ERROR: Low global exclusion count! Yongcheng Zhou (Wed Feb 18 2015 - 18:29:33 CST)
  1. 1ajj_cg_ww.pdb (6632 bytes)
  2. 1ajj_cg_ww.psf (12983 bytes)
  3. 1ajj_cg_ww.ref (6717 bytes)
• Re: LJcorrection and alchemy? Brian Radak (Fri Jan 30 2015 - 14:15:01 CST)
  1. LJcorr.tgz (2113 bytes)
• inconsistency in ABF results for helix unfolding MEHRAN MB (Tue Jan 27 2015 - 17:09:19 CST)
  1. alanine_vacuum.png (12883 bytes)
• Re: problem with water molecules angle in MD simulation Shoresh (Tue Jan 27 2015 - 10:30:54 CST)
  1. waterParm.top (7919 bytes)
• FEP, big variations in dG within a window Jonasson Gabriella (Mon Jan 05 2015 - 09:44:31 CST)
  1. image2.PNG (7271 bytes)
  2. image3.PNG (7617 bytes)
  3. image1.PNG (8643 bytes)
• regarding PME grid setting problem amit banerjee (Sun Jan 04 2015 - 18:31:44 CST)
  1. SK3_wb_eq.conf (3101 bytes)

Last message date: Tue Dec 27 2016 - 20:48:03 CST
Archived on: Tue Dec 27 2016 - 23:22:50 CST

2670 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive