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NAMD-L: By messages with attachments

By messages with attachments

1983 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive

Starting: Tue Jan 01 2019 - 03:25:13 CST
Ending: Thu Dec 31 2020 - 22:29:33 CST

• namdEnergy execution issue -path for namd2 in server Khoualdi Asma Feriel (Wed Dec 30 2020 - 23:23:08 CST)
  1. Script.rtf (2821 bytes)
• Re: Quary resgading Adaptive biasing force Giacomo Fiorin (Thu Oct 08 2020 - 09:36:35 CDT)
  1. image.png (21372 bytes)
• Quary resgading Adaptive biasing force Aashish Bhatt (Thu Oct 08 2020 - 08:43:44 CDT)
  1. image.png (21372 bytes)
  2. win1.in (476 bytes)
• Re: Transition State Search BY NAMD Pawel Kedzierski (Wed Oct 07 2020 - 02:57:04 CDT)
  1. pawel_kedzierski.vcf (571 bytes)
• Drude equilibration Almeida-Hernández, Yasser, Dr. (Mon Oct 05 2020 - 03:08:48 CDT)
  1. step4_equilibration.inp (6471 bytes)
  2. step2_drude.str (267 bytes)
• Re: namd3 on centos 6 Victor Kwan (Sun Sep 20 2020 - 13:07:50 CDT)
  1. 8EF2-4FD5-8BEA-AF4CA58A8FA7.png (1211 bytes)
• Re: namd3 on centos 6 Pratik Narain Srivastava (Sat Sep 19 2020 - 09:04:24 CDT)
  1. 8EF2-4FD5-8BEA-AF4CA58A8FA7.png (1211 bytes)
  2. DB29B52B-8EF2-4FD5-8BEA-AF4CA58A8FA7.png (1211 bytes)
• namd3 on centos 6 Boyan Bonev (Sat Sep 19 2020 - 07:49:07 CDT)
  1. 8EF2-4FD5-8BEA-AF4CA58A8FA7.png (1211 bytes)
• Equilibration of a solvated CNT using C36 zeynab hosseini (Sun Sep 13 2020 - 09:01:52 CDT)
  1. 2020.in (2427 bytes)
• Re:Re: Wrong number of basis-sets stored! è¾›å¿—å®� (Wed Sep 02 2020 - 19:32:23 CDT)
  1. config.ORCA-1.namd (3795 bytes)
  2. config.ORCA-1.namd.log (1800 bytes)
• Re: Re: namd-l digest V1 #2923 Asmi Mahmood (Mon Aug 17 2020 - 02:36:33 CDT)
  1. dummy.out (19044 bytes)
  2. charmrun (578 bytes)
• Re: Asymmetric concentration gradient: non-periodic z-boundary for only ions Gumbart, JC (Sat Aug 15 2020 - 20:23:12 CDT)
  1. tclBC.conf (3458 bytes)
  2. tclBC.tcl (2033 bytes)
• Asymmetric concentration gradient: non-periodic z-boundary for only ions Athreya, Nagendra Bala Murali (Tue Aug 11 2020 - 19:50:48 CDT)
  1. min.namd (1707 bytes)
  2. 1V.namd (2417 bytes)
  3. z_BC.tcl (975 bytes)
  4. eq.namd (2109 bytes)
• RE: Cuboid water box issues Raman Preet Singh (Tue Aug 11 2020 - 13:28:55 CDT)
  1. 2A497EA073BD45AB9E8027E345A093AA.png (144 bytes)
• Cuboid water box issues Raman Preet Singh (Fri Aug 07 2020 - 13:29:06 CDT)
  1. conf.conf (4765 bytes)
• FATAL ERROR: must have same number of LP hosts as lone pairs Selemon Bekele (Wed Jul 22 2020 - 16:33:33 CDT)
  1. Error.log (14278 bytes)
• Pair interaction calculations of the QM/MM system Alex Balaeff (Tue Jul 07 2020 - 18:44:21 CDT)
  1. README.txt (3116 bytes)
• System Drifts Along Z-Axis Bassam Haddad (Fri May 29 2020 - 14:36:49 CDT)
  1. l.namd (2014 bytes)
• Specifying a pull direction with COLVARS Selemon Bekele (Mon May 25 2020 - 23:52:47 CDT)
  1. smd_s0.namd (4445 bytes)
  2. multi.colvars.in (1613 bytes)
  3. drag_3d.namd (1323 bytes)
• NAMD 3.0 alpha, operating system requirements Nicholas M. Glykos (Fri May 22 2020 - 13:19:02 CDT)
  1. smime.p7s (4573 bytes)
• Re: Error: Number of NGauss expected in AddNewGTOs Pawel Kedzierski (Tue Apr 28 2020 - 15:10:01 CDT)
  1. pawel_kedzierski.vcf (571 bytes)
• Umbrella sampling of AA and CNT dissociation, pmf doesn't flatten & reduces over large distances... zeynab hosseini (Wed Apr 15 2020 - 00:07:27 CDT)
  1. files.tar.gz (22236 bytes)
• Re: .coor and .vel output files not generated Khoualdi Asma Feriel (Fri Apr 10 2020 - 00:35:08 CDT)
  1. step6.1_equilibration.inp (9341 bytes)
• difference between numsteps and run in step4_equilibration.inp soodabeh ghaffari (Thu Apr 02 2020 - 14:39:05 CDT)
  1. step4_equilibration.inp (8672 bytes)
• Running on GPU multiple nodes Adupa Vasista (Sun Mar 29 2020 - 04:42:43 CDT)
  1. Solution_eq.log (19008 bytes)
• Re: QM/MM error in the charges Pawel Kedzierski (Fri Feb 28 2020 - 08:06:44 CST)
  1. pawel_kedzierski.vcf (571 bytes)
• Conformation Sampling tutorial: factor of 2 in monitor.sh Alexander Adams (Tue Feb 11 2020 - 13:24:21 CST)
  1. exchange.sh (519 bytes)
• 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 è¾›å¿—å®� (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.sdf (2114 bytes)
  2. 1_autopsf.psf (6650 bytes)
  3. 1.pdb (4690 bytes)
  4. UNL_DB3436.rtf (2181 bytes)
  5. 1_autopsf.pdb (2420 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. pawel_kedzierski.vcf (571 bytes)
  2. runORCA.py (12641 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.psf (666 bytes)
  2. Ion_Ion_JustCoulombic_Attraction_8Ang.pdb (233 bytes)
  3. Ion_Ion_JustCoulombic_Attraction_8Ang.conf (2290 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. image003.png (267 bytes)
  2. image001.png (496 bytes)
  3. image002.png (318 bytes)
• Re: SMD negative forces Joao Ribeiro (Wed Apr 03 2019 - 10:00:17 CDT)
  1. image003.png (266 bytes)
  2. image001.png (495 bytes)
  3. image002.png (317 bytes)
• Re: NAMD support for lone pairs Tabitha Nobel (Mon Mar 11 2019 - 17:15:45 CDT)
  1. test.crd (3473 bytes)
  2. output_min.crd (3535 bytes)
• Re: Minimization Error ê¹€ë¯¼ìž¬ (Tue Mar 05 2019 - 05:02:52 CST)
  1. 1ca2min.stderr (381 bytes)
  2. 1ca2min.stdout (602 bytes)
  3. runmin (75 bytes)
  4. 1ca2_min.log (3271 bytes)
• Minimization Error ê¹€ë¯¼ìž¬ (Tue Mar 05 2019 - 00:31:36 CST)
  1. 1ca2_min.log (3271 bytes)
• Running NAMD on Linux Cluster ê¹€ë¯¼ìž¬ (Tue Feb 26 2019 - 09:22:37 CST)
  1. testx.stdout (757 bytes)
  2. testy.stdout (758 bytes)
  3. testy.stderr (243 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)

Last message date: Thu Dec 31 2020 - 22:29:33 CST
Archived on: Thu Dec 31 2020 - 23:17:15 CST

1983 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive