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NAMD-L: By messages with attachments

By messages with attachments

2690 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive

Starting: Sun Jan 01 2017 - 04:00:35 CST
Ending: Mon Dec 31 2018 - 09:42:31 CST

• run MD simulation in NAMD using stages file strategy or all in one file ? L- (Thu Dec 13 2018 - 10:12:13 CST)
  1. allinone.txt (3376 bytes)
• Re: NAMD QM/MM alchemical free energy change capabilities? Brian Radak (Tue Nov 27 2018 - 08:26:34 CST)
  1. 1495766834.jpg (5529 bytes)
• NAMD QM/MM alchemical free energy change capabilities? Braden Kelly (Mon Nov 26 2018 - 22:07:33 CST)
  1. 1495766834.jpg (5529 bytes)
• ffTK torsion scan convergence using Gaussian. Dipak Balasaheb Sanap (Mon Nov 12 2018 - 18:08:12 CST)
  1. FRA.scan9.pos.gau (1401 bytes)
• vacuum condition in config file soroush ziaei (Fri Oct 19 2018 - 13:58:37 CDT)
  1. 0.namd (641 bytes)
  2. 1.namd (745 bytes)
  3. 2.namd (1235 bytes)
• Re: Broken Structure after reverting coarse-grained system to all-atom system Rabeta Yeasmin (Tue Jul 10 2018 - 09:46:07 CDT)
  1. resid7.png (7868 bytes)
• Problem in generating psf Srijita Paul (Thu May 31 2018 - 01:25:39 CDT)
  1. dodine_vega.pdb (4974 bytes)
  2. top_dodine.rtf (9180 bytes)
• Hard wall on Z direction for ions Fateme Ghadirian (Mon May 14 2018 - 09:06:31 CDT)
  1. z_BC.tcl (1032 bytes)
  2. minimization_Equilibrium.conf (2341 bytes)
• Problem generating pdb psf of ATP Srijita Paul (Mon May 14 2018 - 02:33:43 CDT)
  1. atp_namd.pdb (3043 bytes)
  2. atp_new.pdb (3605 bytes)
  3. atp_new.psf (12788 bytes)
• Re: Re: vmd-l: Fwd: FEP with intermediary segments Francesco Pietra (Sat May 05 2018 - 01:21:23 CDT)
  1. summary.png (10942 bytes)
• Aromatic rings don't maintain the planarity during the heating Serena Vittorio (Fri May 04 2018 - 11:14:30 CDT)
  1. Heat.namd (1623 bytes)
• Re: FEP slowdown Francesco Pietra (Tue Apr 24 2018 - 08:51:02 CDT)
  1. probability.1.png (7429 bytes)
  2. energy.1.png (6520 bytes)
• UNABLE TO FIND ANGLE PARAMETERS FOR CT OS HO (ATOMS 23662 23661 23656) Ashutosh Shandilya (Fri Mar 02 2018 - 13:55:43 CST)
  1. 1.inp (1761 bytes)
  2. 1_new.inp (1835 bytes)
• periodic cell has become too small for original patch grid Ashutosh Shandilya (Fri Mar 02 2018 - 13:55:10 CST)
  1. min1.namd (1643 bytes)
  2. min2.namd (1695 bytes)
  3. min3.namd (1485 bytes)
  4. nvt.namd (1734 bytes)
• FEP minimum requirements Francesco Pietra (Thu Mar 01 2018 - 03:05:22 CST)
  1. summary.png (12765 bytes)
• Re: Srijita Paul (Fri Feb 16 2018 - 06:42:56 CST)
  1. normal_job.namd (358 bytes)
  2. main_job.conf (520 bytes)
• namd2 GPU error Miraj Naik (Tue Feb 13 2018 - 22:43:10 CST)
  1. step4_equilibration_NVT.inp (8021 bytes)
  2. submit_gpu.sh (362 bytes)
• (no subject) Srijita Paul (Tue Feb 13 2018 - 05:06:51 CST)
  1. main_job.conf (520 bytes)
  2. normal_job.namd (358 bytes)
• Re: Ways to find water molecules passing through the water channel in lipid bilayer Bassam Haddad (Thu Jan 18 2018 - 18:46:46 CST)
  1. atom_traj.tcl (531 bytes)
• Re: Script for Terachem QMMM Haohao Fu (Thu Dec 14 2017 - 07:13:47 CST)
  1. namd_xtb.py (7810 bytes)
• Free MD simulation (Production run) Roshan Shrestha (Fri Sep 08 2017 - 02:32:50 CDT)
  1. sim_free.namd (2202 bytes)
• No minimized system after running minimization in NAMD Roshan Shrestha (Thu Sep 07 2017 - 09:17:02 CDT)
  1. minimization.conf (2176 bytes)
• Production run after equilibration Roshan Shrestha (Tue Aug 29 2017 - 05:38:00 CDT)
  1. equil.conf (2968 bytes)
• Re: make psf error for ligand Natasha Gupta (Fri Aug 25 2017 - 05:37:38 CDT)
  1. rscb.pdb (3397 bytes)
  2. mkpsf.log (17478 bytes)
  3. mkpsf1.tcl (1509 bytes)
• Re: Creating psf file for ligand Roshan Shrestha (Thu Aug 24 2017 - 12:58:07 CDT)
  1. ZINC05.mol2 (7086 bytes)
  2. ZNC05.pdb (4428 bytes)
• Re: Creating psf file for ligand Roshan Shrestha (Sat Aug 12 2017 - 09:38:59 CDT)
  1. 8093.mol2 (6453 bytes)
  2. convert_out.pdb (8219 bytes)
• Re: veldcdfile command Jérôme Hénin (Thu Jun 29 2017 - 07:11:45 CDT)
  1. veldcdfile.patch (1747 bytes)
• Re: veldcdfile command Giacomo Fiorin (Wed Jun 28 2017 - 13:36:43 CDT)
  1. veldcdfile.patch (1521 bytes)
• Re: veldcdfile command Jérôme Hénin (Wed Jun 28 2017 - 11:41:21 CDT)
  1. veldcdfile.patch (2328 bytes)
• Re: veldcdfile command Jérôme Hénin (Wed Jun 28 2017 - 11:05:58 CDT)
  1. veldcdfile.patch (1524 bytes)
• Re: coarse-grained simulations with errors "Atoms moving too fast" and "low global exclusion" Yaxin An (Fri Jun 09 2017 - 10:38:33 CDT)
  1. image.png (3514 bytes)
  2. image.png (3444 bytes)
  3. image.png (275 bytes)
  4. image.png (117 bytes)
• Keeping potassium ions out of an area during equilibration Charles Hoying (Mon Jun 05 2017 - 22:57:40 CDT)
  1. keep_water_out.tcl (8617 bytes)
• Re: namd 2.12 and plumed 2.3 Vermaas, Joshua (Tue May 02 2017 - 10:22:01 CDT)
  1. combineddiff.txt (9994 bytes)
• compilation of NAMD 2.12 fails Vlad Cojocaru (Thu Apr 27 2017 - 10:02:19 CDT)
  1. 6.7.1_openmpi-2.1.0_gnu-4.8.5.log (67172 bytes)
• psfgen giving wrong structure in the autopdb file Harish Srinivasan (Thu Apr 06 2017 - 01:37:29 CDT)
  1. dodecylsulphate.rtf (2285 bytes)
  2. dodecylsulphate2.pdb (7440 bytes)
  3. dodecylsulphate2_autopsf.psf (9768 bytes)
  4. dodecylsulphate2_autopsf.pdb (3368 bytes)
• patch hem_chandra_at_iitg.ernet.in (Mon Mar 27 2017 - 23:28:53 CDT)
  1. boc.str (3914 bytes)
  2. wwl.pdb (2666 bytes)
• Problem in NAMD QMMM Kshatresh Dutta Dubey (Sat Mar 25 2017 - 13:37:25 CDT)
  1. out.log (10344 bytes)
  2. config.ORCA.namd (5398 bytes)
• Re: AW: Scaling behaviour of NAMD on hosts with GPU accelrators Maxime Boissonneault (Fri Mar 24 2017 - 06:42:04 CDT)
  1. benchmark_scaling_namd20150917_k80.csv (1174 bytes)
• Re: problems mutating HID to TYR for free energy calculations Nehad Elsalamouny (Tue Mar 07 2017 - 16:50:32 CST)
  1. h2y.rtf (8720 bytes)
  2. ATT00001.htm (6395 bytes)
• problems mutating HID to TYR for free energy calculations Nehad Elsalamouny (Tue Mar 07 2017 - 04:27:28 CST)
  1. xxxx.pdb (1554 bytes)
  2. ATT00001.htm (215 bytes)
  3. h2y.pdb (2880 bytes)
  4. ATT00002.htm (516 bytes)
• AW: vmd-l: Building NAMD 2.12 from Source with IB and CUDA Greipel.Joachim_at_mh-hannover.de (Thu Mar 02 2017 - 05:53:58 CST)
  1. smime.p7s (5980 bytes)
• Regarding Error on HB2 Obayed Ullah (Mon Feb 20 2017 - 18:48:56 CST)
  1. trif_ionized_min_dynamic.conf (1892 bytes)
• Re: Npt lipid simulation with electrostatics 2 Life Sciences Inc (Fri Feb 17 2017 - 11:04:12 CST)
  1. volume.jpg (27833 bytes)
• Re: Npt lipid simulation with electrostatics 2 Life Sciences Inc (Fri Feb 17 2017 - 10:52:36 CST)
  1. volume.jpg (27833 bytes)
• Compiling charm/NAMD with an alternative gcc, e.g. gcc 6.x Greipel.Joachim_at_mh-hannover.de (Mon Feb 06 2017 - 08:54:08 CST)
  1. smime.p7s (5980 bytes)
• Solvation free energy difference of alchemical transformation of K+ into Na+ Abhishek Kumar Singh (Tue Jan 10 2017 - 05:09:01 CST)
  1. derivate_vs___values (255 bytes)
• dcd to pdb conversion Srijita Paul (Wed Jan 04 2017 - 06:18:21 CST)
  1. dcdtopdb.tcl (271 bytes)

Last message date: Mon Dec 31 2018 - 09:42:31 CST
Archived on: Mon Dec 31 2018 - 23:21:39 CST

2690 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive