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NAMD-L: By messages with attachments

By messages with attachments

1614 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive

Starting: Fri Jan 03 2020 - 07:25:25 CST
Ending: Thu Dec 30 2021 - 09:20:14 CST

• Re: SMD: Fixing centroid Almeida-Hernández, Yasser, Dr. (Mon Dec 20 2021 - 07:00:55 CST)
  1. pulling_colvars_test.in (1983 bytes)
• tclForce not recognizing group option during cphmd job Diship Srivastava (Wed Dec 15 2021 - 23:42:58 CST)
  1. f.tcl (1922 bytes)
• Error in running multiple-walkers metadynamics at Bluewaters Chen, Charles (Wed Dec 08 2021 - 18:29:27 CST)
  1. OMPF.inp (5595 bytes)
  2. input.in (1371 bytes)
  3. job0.conf (1990 bytes)
  4. base_job.tcl (1254 bytes)
• FEP calculation for Binding of a potassium ion to 18Q=80=93crown=E2=80=936?= SYEDA SABIHA SULTANA LUBNA . (Thu Nov 25 2021 - 04:14:03 CST)
  1. forward.namd (2623 bytes)
  2. backward.namd (2705 bytes)
  3. backward.namd (2610 bytes)
  4. forward.namd (2718 bytes)
• residue_rmsd.tcl script Alexei Rossokhin (Thu Nov 25 2021 - 02:15:39 CST)
  1. residue_rmsd.tcl (1899 bytes)
• Re: vmd-l: Re: namd minimization looking for wrong angle Francesco Pietra (Fri Nov 19 2021 - 10:55:59 CST)
  1. chcl3.psf (1057 bytes)
  2. chcl3.pdb (445 bytes)
  3. 1009279.rtf (399 bytes)
• colvars: Too many iterations in routine jacobi. Ashutosh Shandilya (Wed Nov 17 2021 - 09:58:33 CST)
  1. input_file.tcl (10927 bytes)
• Re: RMSD and RMSF of ligand Only Mi Yang (Thu Oct 28 2021 - 08:35:40 CDT)
  1. RMSF_step3copy.tcl (1158 bytes)
• Error: keyword "abf" found without configuration Ashutosh Shandilya (Wed Oct 27 2021 - 14:43:12 CDT)
  1. eABF.tcl (10887 bytes)
• [containerising NAMD with Singularity] Maxim Abalenkov (Wed Oct 13 2021 - 04:28:36 CDT)
  1. t.295873.log (2123 bytes)
  2. centos.def (4281 bytes)
  3. 01.log (743 bytes)
  4. namd.slurm (1104 bytes)
• Re: Problem with speed of QMMM (namd2-ORCA) Herald Delis (Sun Sep 12 2021 - 00:22:07 CDT)
  1. image.gif (42 bytes)
• Re: Problem with speed of QMMM (namd2-ORCA) Marcelo C. R. Melo (Sat Sep 11 2021 - 00:27:46 CDT)
  1. image.gif (42 bytes)
• Re: Problem with speed of QMMM (namd2-ORCA) Herald Delis (Thu Sep 09 2021 - 19:59:56 CDT)
  1. image.gif (42 bytes)
• Re: Problem with speed of QMMM (namd2-ORCA) Marcelo C. R. Melo (Thu Sep 09 2021 - 12:09:00 CDT)
  1. image.gif (42 bytes)
• Problem with speed of QMMM (namd2-ORCA) Herald Delis (Thu Sep 09 2021 - 05:51:14 CDT)
  1. image.gif (42 bytes)
• RE: Unrealistically High Keq in eABF Seperation Ishaan Roy (Wed Sep 08 2021 - 13:46:47 CDT)
  1. B93E01B608D94097BD9FC540C8AB8BF0.png (159 bytes)
• RE: Unrealistically High Keq in eABF Seperation Ishaan Roy (Thu Aug 26 2021 - 02:28:47 CDT)
  1. E5916A1806AB45B69588CDD3A9BF60CF.png (13137 bytes)
• Re: Unrealistically High Keq in eABF Seperation Peter Freddolino (Wed Aug 25 2021 - 22:27:46 CDT)
  1. E5916A1806AB45B69588CDD3A9BF60CF.png (13137 bytes)
• Unrealistically High Keq in eABF Seperation Ishaan Roy (Tue Aug 24 2021 - 17:23:39 CDT)
  1. E5916A1806AB45B69588CDD3A9BF60CF.png (13137 bytes)
• Re: Asymmetric concentration gradient Gumbart, JC (Mon Aug 23 2021 - 23:05:19 CDT)
  1. tclBC.conf (3458 bytes)
  2. tclBC.tcl (2033 bytes)
• Re: Getting the z coordinate Pawel Kedzierski (Mon May 17 2021 - 12:17:31 CDT)
  1. pawel_kedzierski.vcf (571 bytes)
• Re: Meaning of the warning: Low global exclusion count! Pawel Kedzierski (Thu Apr 22 2021 - 08:21:08 CDT)
  1. pawel_kedzierski.vcf (571 bytes)
• Meaning of the warning: Low global exclusion count! Pawel Kedzierski (Wed Apr 21 2021 - 06:01:05 CDT)
  1. pawel_kedzierski.vcf (571 bytes)
• Re: Problem with running NAMD config file Tiglath Moradkhan (Thu Feb 11 2021 - 11:28:19 CST)
  1. CSApoA1.conf (3546 bytes)
• NAMD speed and Scaling raghav singh (Mon Jan 25 2021 - 06:02:52 CST)
  1. MD.1.namd (2241 bytes)
  2. pjob_MD1.sh (299 bytes)
• 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)

Last message date: Thu Dec 30 2021 - 09:20:14 CST
Archived on: Fri Dec 31 2021 - 23:17:12 CST

1614 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive