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NAMD-L: By messages with attachments

By messages with attachments

3174 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive

Starting: Wed Jan 01 2014 - 05:18:45 CST
Ending: Tue Dec 29 2015 - 07:12:19 CST

• 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)
• Re: Colvar: minimal distance between 2 groups of atoms Ajasja Ljubetič (Mon Nov 17 2014 - 11:30:45 CST)
  1. part (9260 bytes)
  2. part (29688 bytes)
• Re: Colvar: minimal distance between 2 groups of atoms Ajasja Ljubetič (Mon Nov 17 2014 - 10:28:20 CST)
  1. image.png (9260 bytes)
  2. image.png (29688 bytes)
• Re: vmd-l: making psf files Zeinab Emami (Mon Oct 13 2014 - 04:55:06 CDT)
  1. Ethane_e.pdb (1722 bytes)
• 2-residue patch for Asn-Lys side chain amide bond Kenno Vanommeslaeghe (Fri Jul 25 2014 - 12:20:46 CDT)
  1. dkam.str (1845 bytes)
• 2-residue patch for hydrocarbon staple Kenno Vanommeslaeghe (Thu Jul 24 2014 - 15:48:52 CDT)
  1. k2hc7staple.str (5414 bytes)
• Loading and analysis of DCD file (~300 MB) Stephan Grein (Thu Jul 24 2014 - 06:18:45 CDT)
  1. low_wrappers.tcl (5423 bytes)
• AW: Should PME be used for electrostatic interaction energy calculations? Norman Geist (Thu Jun 19 2014 - 02:46:48 CDT)
  1. ng_n07_cutoff9_noPME.dcd.png (13760 bytes)
  2. ng_n07_cutoff9_withPME.dcd.png (9137 bytes)
• Constraint failure in RATTLE algorithm Douglas Houston (Wed Jun 18 2014 - 12:29:48 CDT)
  1. mdrun.conf (3559 bytes)
• Re: About electrostatic treatment Mo Chen (Fri May 30 2014 - 19:39:31 CDT)
  1. gromacs.jpg (19641 bytes)
• Re: FixedAtoms and Reference group in spinangle colvar nicolas martin (Thu May 22 2014 - 07:06:08 CDT)
  1. spin-dihe-EB.png (102797 bytes)
• Re: Teflon New Residue Kenno Vanommeslaeghe (Fri May 02 2014 - 12:21:09 CDT)
  1. perfluorohexane.mol2 (1108 bytes)
  2. perfluorohexane_cgenff.str (4109 bytes)
  3. perfluorohexane_adjust_ch.str (3828 bytes)
• Re: Help to solve the error Flora Chettiar (Thu Mar 27 2014 - 01:47:09 CDT)
  1. config_file_of_vmd_namd.txt (2958 bytes)
• Require Suggestion amit banerjee (Tue Feb 18 2014 - 23:39:40 CST)
  1. Consensus_ws_eq.log (5707 bytes)
  2. Consensus_ws_eq.conf (2583 bytes)
• Re: AW: Dihedrals multiplicity! Anna Borlsky (Sat Feb 15 2014 - 04:34:49 CST)
  1. cou.par (9196 bytes)
  2. cou.top (7604 bytes)
• unsubscribe Zailo Leite (Fri Feb 14 2014 - 11:20:04 CST)
  1. 0x202F0355.asc (1736 bytes)
• Re: ABF simulations Aron Broom (Mon Feb 10 2014 - 11:20:54 CST)
  1. jpg.counts.abf_low.jpeg (18203 bytes)
  2. jpg.pmfs_low.jpeg (22856 bytes)
• Re: AW: Re: Various questions Douglas Houston (Tue Feb 04 2014 - 07:26:05 CST)
  1. GetNAMDdims.ksh (1213 bytes)

Last message date: Tue Dec 29 2015 - 07:12:19 CST
Archived on: Thu Dec 31 2015 - 23:22:24 CST

3174 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive