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NAMD-L: By messages with attachments

By messages with attachments

2431 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive

Starting: Mon Jan 01 2018 - 09:14:56 CST
Ending: Mon Dec 30 2019 - 20:12:28 CST

• Re: fatal error regarding parameters mohammad goodarzi (Tue Dec 10 2019 - 12:15:01 CST)
  1. BNZ.pdb (810 bytes)
• Re: looping on multiple dcds in namd configuration file SHIVAM TIWARI (Fri Nov 15 2019 - 06:25:46 CST)
  1. interaction.namd (1239 bytes)
• Fwd: running NAMD with AMBER inputs Rui Chen (Sun Sep 01 2019 - 13:13:12 CDT)
  1. min.conf (3387 bytes)
• Re: Re: FATAL ERROR: Must have either an initial temperature or a velocity file 辛志宏 (Tue Jul 30 2019 - 20:50:47 CDT)
  1. 07-30_21-43-54.png (7848 bytes)
• namdstats.tcl problem Rui Chen (Wed Jul 24 2019 - 17:24:46 CDT)
  1. namdstats.tcl (3455 bytes)
• Getting the topology,PSF files Adupa Vasista (Thu Jul 04 2019 - 14:54:25 CDT)
  1. 1.pdb (4690 bytes)
  2. 1.sdf (2114 bytes)
  3. 1_autopsf.psf (6650 bytes)
  4. 1_autopsf.pdb (2420 bytes)
  5. UNL_DB3436.rtf (2181 bytes)
• readmol2 warning: non-unique atoms were renamed. Adupa Vasista (Sat Jun 29 2019 - 11:30:25 CDT)
  1. PDP.pdb (18225 bytes)
• Re: Bug in NAMD Pawel Kedzierski (Sat Jun 22 2019 - 04:52:43 CDT)
  1. pawel_kedzierski.vcf (571 bytes)
• Re: Bug in NAMD Pawel Kedzierski (Fri Jun 21 2019 - 07:01:03 CDT)
  1. pawel_kedzierski.vcf (571 bytes)
• Re: Bug in NAMD (was: Big oscillations during QM/MM minimization) Pawel Kedzierski (Thu Jun 20 2019 - 10:35:11 CDT)
  1. pawel_kedzierski.vcf (571 bytes)
• Re: Bug in NAMD (was: Big oscillations during QM/MM minimization) Pawel Kedzierski (Thu Jun 20 2019 - 10:11:19 CDT)
  1. pawel_kedzierski.vcf (571 bytes)
• Re: Bug in NAMD Pawel Kedzierski (Thu Jun 20 2019 - 08:23:43 CDT)
  1. pawel_kedzierski.vcf (571 bytes)
• Bug in NAMD (was: Big oscillations during QM/MM minimization) Pawel Kedzierski (Tue Jun 18 2019 - 01:47:24 CDT)
  1. runORCA.py (12641 bytes)
  2. pawel_kedzierski.vcf (571 bytes)
• colvar setting, targetcenters not working Jiali Wang (Sun Jun 16 2019 - 20:16:49 CDT)
  1. colvars.conf (917 bytes)
  2. outputsmd2.colvars.traj (19114 bytes)
• FATAL ERROR: Periodic cell has become too small for original patch grid! Adupa Vasista (Sun May 26 2019 - 07:07:39 CDT)
  1. water.conf (3009 bytes)
• Big oscillations during QM/MM minimization Pawel Kedzierski (Tue May 07 2019 - 08:53:18 CDT)
  1. pawel_kedzierski.vcf (571 bytes)
• Electrostatic interaction of 2 ions Fateme Ghadirian (Fri Apr 12 2019 - 09:33:08 CDT)
  1. Ion_Ion_JustCoulombic_Attraction_8Ang.conf (2290 bytes)
  2. Ion_Ion_JustCoulombic_Attraction_8Ang.pdb (233 bytes)
  3. Ion_Ion_JustCoulombic_Attraction_8Ang.psf (666 bytes)
  4. Ion_Ion_JustCoulombic_Attraction_8Ang.vel (162 bytes)
• Re: SMD negative forces Joao Ribeiro (Wed Apr 03 2019 - 10:18:06 CDT)
  1. image001.png (496 bytes)
  2. image002.png (318 bytes)
  3. image003.png (267 bytes)
• Re: SMD negative forces Joao Ribeiro (Wed Apr 03 2019 - 10:00:17 CDT)
  1. image001.png (495 bytes)
  2. image002.png (317 bytes)
  3. image003.png (266 bytes)
• Re: NAMD support for lone pairs Tabitha Nobel (Mon Mar 11 2019 - 17:15:45 CDT)
  1. output_min.crd (3535 bytes)
  2. test.crd (3473 bytes)
• Re: Minimization Error 김민재 (Tue Mar 05 2019 - 05:02:52 CST)
  1. 1ca2_min.log (3271 bytes)
  2. 1ca2min.stderr (381 bytes)
  3. 1ca2min.stdout (602 bytes)
  4. runmin (75 bytes)
• Minimization Error 김민재 (Tue Mar 05 2019 - 00:31:36 CST)
  1. 1ca2_min.log (3271 bytes)
• Running NAMD on Linux Cluster 김민재 (Tue Feb 26 2019 - 09:22:37 CST)
  1. testy.stdout (758 bytes)
  2. testy.stderr (243 bytes)
  3. testx.stdout (757 bytes)
  4. testx.stderr (1412 bytes)
• Re: Stochastic velocity rescaling for Free Energy calculations Brian Radak (Mon Feb 25 2019 - 12:05:22 CST)
  1. 1495766834.jpg (5529 bytes)
• Stochastic velocity rescaling for Free Energy calculations Braden Kelly (Sat Feb 23 2019 - 15:21:37 CST)
  1. 1495766834.jpg (5529 bytes)
• RE: run MD simulation in NAMD using stages file strategy or allin one file ? soroush ziaei (Sat Jan 26 2019 - 14:26:04 CST)
  1. run.sh (295 bytes)
• hbond restraint simulation Prabir Khatua (Fri Jan 25 2019 - 13:19:24 CST)
  1. hbond-new.in (6663 bytes)
• 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)

Last message date: Mon Dec 30 2019 - 20:12:28 CST
Archived on: Tue Dec 31 2019 - 23:21:07 CST

2431 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive