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NAMD-L: By messages with attachments

By messages with attachments

3952 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive

Starting: Tue Jan 02 2007 - 09:52:55 CST
Ending: Wed Dec 31 2008 - 05:25:21 CST

• Re: namd cvs compilation BIN ZHANG (Mon Dec 01 2008 - 11:59:39 CST)
  1. 1.conf (2321 bytes)
• H-bond occupancy in nucleic acids Tianjiao Wang (Thu Nov 20 2008 - 10:08:27 CST)
  1. hbonds.tcl (20260 bytes)
• ABF:problems with calculating Free Energy Profile supram_at_nankai.edu.cn (Sun Nov 16 2008 - 20:55:39 CST)
  1. bcdlglu.abf (14219 bytes)
• NAMD Simulation error Anirban Ghosh (Fri Nov 14 2008 - 02:36:16 CST)
  1. CG.conf (2737 bytes)
• NAMD Simulation error Anirban Ghosh (Wed Nov 12 2008 - 22:41:07 CST)
  1. CG.conf (2737 bytes)
• Re: Atoms moving too fast OR constraint failure in RATTLE algorithm Diego Alejandro Vargas (Sat Nov 08 2008 - 17:31:30 CST)
  1. ser39ala_wb_mn.xst (2047 bytes)
  2. ser39ala_wb_eq.xst (172 bytes)
• Re: ABF - using gyration Jerome Henin (Tue Oct 28 2008 - 15:11:43 CDT)
  1. abf_script.tcl (21731 bytes)
  2. gyration.tcl (2758 bytes)
• ABF backbone dihedral Sébastien Légaré (Tue Oct 28 2008 - 11:44:21 CDT)
  1. helix.tcl (8212 bytes)
• Backbone dihedral ABF Sébastien Légaré (Tue Oct 28 2008 - 11:50:02 CDT)
  1. helix.tcl (8212 bytes)
• Using NAMD to calculate pair energy with many subset permutations brmorgan_at_clarku.edu (Wed Oct 15 2008 - 13:08:42 CDT)
  1. energy_batch.namd (2557 bytes)
• Problem with creating psf file from structure made by inorganic builder Anneta Tzampazi (Fri Oct 03 2008 - 04:43:19 CDT)
  1. pyramida.top (317 bytes)
• FW: psf generation for a small non-peptide molecule - again CHINDEA Vlad (Mon Sep 29 2008 - 17:21:16 CDT)
  1. azi.pdb (11017 bytes)
  2. unk_azi.xbgf (1974 bytes)
• Namd water density jouko_at_uchicago.edu (Mon Sep 22 2008 - 21:36:11 CDT)
  1. bakforeq.conf.md (4458 bytes)
• Re: need help on CG modelling Nicolas Sapay (Mon Sep 22 2008 - 13:59:16 CDT)
  1. nsapay.vcf (283 bytes)
• Re: need help on CG modelling Nicolas Sapay (Mon Sep 22 2008 - 12:34:47 CDT)
  1. nsapay.vcf (283 bytes)
• TCL Forces : OUT OF MEMORY BIN ZHANG (Fri Sep 12 2008 - 13:38:17 CDT)
  1. derv.tcl (6532 bytes)
  2. wham_1d.tcl (2613 bytes)
• NAMD compilation / TACC Ranger Arturas Ziemys (Thu Aug 28 2008 - 11:25:14 CDT)
  1. Ranger-2.log.gz (5595 bytes)
• Re: How to write gradual heating config file Hyundeok Song (Mon Aug 25 2008 - 19:30:26 CDT)
  1. heat7.ps (14452 bytes)
• Re: unwanted bonds in .pdb file while using molefacture Subhashis Biswas (Wed Aug 06 2008 - 14:23:23 CDT)
  1. GCTiO2.pdb (9872 bytes)
• Constraining center of mass of monomers S.K. Ghosh (Wed Jul 16 2008 - 17:45:57 CDT)
  1. smd.tcl (1548 bytes)
• memory overflow problem of Tcl scripting when dealing with trajectories bo liu (Wed Jul 16 2008 - 03:16:31 CDT)
  1. dipole_profile.tcl (6794 bytes)
• Re: Rise in Total Energy in NVE S.K. Ghosh (Wed Jul 09 2008 - 10:25:35 CDT)
  1. energy.log (719 bytes)
• Running minimization, heating and FEP simulation within the same configuration file. Jawahar Neelankatan (Tue Jun 24 2008 - 20:28:21 CDT)
  1. min_heat_eq_FEP.conf (2590 bytes)
• Different Hbonds values on different machines using same script for same trajectories sunita gupta (Mon Jun 09 2008 - 02:29:57 CDT)
  1. hbonds.tcl (20260 bytes)
  2. hbonds1.txt (4685 bytes)
  3. hbonds2.txt (2876 bytes)
• Bond energy become Zero!!! Ming (Thu Jun 05 2008 - 04:17:01 CDT)
  1. CH4.top (2802 bytes)
  2. CH4.par (4084 bytes)
  3. CH4_try.psf (1092 bytes)
  4. CH4_try.pdb (452 bytes)
• Re: The correct topology/parameter file and pgn S.K. Ghosh (Wed Jun 04 2008 - 13:48:41 CDT)
  1. btn.inp (2912 bytes)
• Problem with TclBC when run in more than one processor fett_at_vtr.net (Wed Jun 04 2008 - 12:08:57 CDT)
  1. eF_water_test.conf (3874 bytes)
• Re: Error Parsing Config File MIke S (Mon May 26 2008 - 15:46:19 CDT)
  1. trial.conf (5718 bytes)
• Energy plot script Alexandre A. Vakhrouchev (Wed May 14 2008 - 22:11:19 CDT)
  1. plot_energy.sh.gz (1205 bytes)
• What does "cellOrigin" really mean? bo liu (Wed Apr 23 2008 - 05:48:45 CDT)
  1. pic1.JPG (21336 bytes)
• What does "cellOrigin" really mean? bo liu (Fri Apr 18 2008 - 09:38:56 CDT)
  1. pic1.JPG (21336 bytes)
• FEP: FATAL ERROR: Periodic cell has become too small for original patch grid! List (Wed Mar 12 2008 - 13:29:38 CDT)
  1. fep.conf (2878 bytes)
• NAMD stops running without error messages or termination Yinglong Miao (Mon Mar 03 2008 - 17:18:12 CST)
  1. NAMD.tcl (1904 bytes)
• protein_RNA simulation sripad chandan (Sat Mar 01 2008 - 08:43:22 CST)
  1. xmin.conf (2396 bytes)
  2. comp.pgn.txt (703 bytes)
• namd_minimize sripad chandan (Sun Feb 24 2008 - 10:51:47 CST)
  1. 1tbc_c_ws_eq.conf (1278 bytes)
• Alchemical FEP NAMD tutorial - problems with reproducing the results Jawahar Neelankatan (Mon Feb 18 2008 - 21:25:54 CST)
  1. tyr2ala.pdb (4637 bytes)
• ABF question Matthew Davies (Wed Feb 13 2008 - 11:00:44 CST)
  1. abf.dat (660 bytes)
• Re: catDCD 32 bit Vs. 64 bit Version Philip Peartree (Thu Feb 07 2008 - 09:28:15 CST)
  1. dcd_convert.tcl (202 bytes)
• how to minimize the energy of a protein using CHARMM FF in NAMD Kalyan chaitanya (Thu Feb 07 2008 - 09:29:08 CST)
  1. input-file.doc (26624 bytes)
  2. standard_parameter_file.txt (706 bytes)
• Tests not running for Charm++ Myrinet with MPICH-MX brmorgan_at_clarku.edu (Wed Jan 23 2008 - 14:35:05 CST)
  1. mach.sh (939 bytes)
• Re: Segmentation violation when running without an internet connection Robert Brunner (Thu Dec 20 2007 - 14:45:41 CST)
  1. smime.p7s (2417 bytes)
• Re: problems replicating a DOPC membrane Richard Swenson (Thu Nov 29 2007 - 14:57:35 CST)
  1. cla_psf.tcl (383 bytes)
  2. dopc_psf.tcl (783 bytes)
  3. fix.tcl (1075 bytes)
  4. reformat.sh (951 bytes)
  5. sod_psf.tcl (379 bytes)
  6. system_psf.tcl (545 bytes)
  7. water_psf.tcl (520 bytes)
• Re: Is there solution to numerical inaccuracy Alok Juneja (Fri Nov 23 2007 - 12:14:01 CST)
  1. comparision.pdf (6353 bytes)
  2. B1-B2.pdf (2997 bytes)
• Re: Replica Exchange NAMD John R. Dowdle (Mon Nov 19 2007 - 20:16:43 CST)
  1. signature.asc (190 bytes)
• heat flux when using langevin dynamics Philipp Schön (Thu Nov 01 2007 - 09:12:56 CDT)
  1. smime.p7s (1764 bytes)
• Errors during equilibration: segmentation fault and bad global exclusion count Ambrish (Tue Oct 23 2007 - 01:45:05 CDT)
  1. equil_mode2.namd (2817 bytes)
• (no subject) ramya narasimhan (Tue Oct 23 2007 - 00:45:16 CDT)
  1. resmd.conf (1590 bytes)
• Molecule drifts and high average RMSD per residue Ambrish (Mon Oct 08 2007 - 11:02:49 CDT)
  1. npt_model1.namd (1635 bytes)
• question regarding nearest-image resolution in NAMD Vincent Kraeutler (Mon Sep 03 2007 - 03:23:24 CDT)
  1. signature.asc (250 bytes)
• Re: Recommended solvation box size Vincent Kraeutler (Wed Aug 29 2007 - 07:46:48 CDT)
  1. signature.asc (250 bytes)
• Re: Re: pressure vs density tip3p Vincent Kraeutler (Mon Aug 27 2007 - 16:55:47 CDT)
  1. signature.asc (250 bytes)
• Re: pressure vs density tip3p Roy Kimura (Mon Aug 27 2007 - 16:04:24 CDT)
  1. roy.kimura.vcf (262 bytes)
• pressure vs density tip3p Roy Kimura (Mon Aug 27 2007 - 15:54:40 CDT)
  1. roy.kimura.vcf (262 bytes)
• Re: setting solvent density during solvation jestin mandumpal (Mon Aug 27 2007 - 01:05:32 CDT)
  1. tip5p.top (310 bytes)
  2. tip5p.pdb (433 bytes)
• Re: How to implement an additional interaction potential? Vincent Kraeutler (Thu Aug 23 2007 - 07:53:05 CDT)
  1. signature.asc (250 bytes)
• How to implement an additional interaction potential? Philipp Schön (Thu Aug 23 2007 - 07:00:12 CDT)
  1. smime.p7s (1764 bytes)
• Re: energy drift in NVE Vincent Kraeutler (Mon Aug 20 2007 - 02:22:49 CDT)
  1. signature.asc (250 bytes)
• Code question: Partitioning the patch contents into water and non-water Vincent Kraeutler (Fri Aug 17 2007 - 04:01:24 CDT)
  1. signature.asc (250 bytes)
• Re: Re: NAMD: Exiting Prematurely Vincent Kraeutler (Wed Aug 15 2007 - 14:06:44 CDT)
  1. signature.asc (250 bytes)
• How to avoid => ERROR: Step 100920 cell rescaling factor limited. Philipp Schön (Mon Aug 13 2007 - 07:28:39 CDT)
  1. smime.p7s (1764 bytes)
• Re: Storage of large files Vincent Kraeutler (Thu Aug 09 2007 - 04:03:32 CDT)
  1. signature.asc (250 bytes)
• Re: Is very slow heating "bad"? Vincent Kraeutler (Sat Aug 04 2007 - 11:06:11 CDT)
  1. signature.asc (250 bytes)
• no effect on velocity scaling Philipp Schön (Fri Aug 03 2007 - 02:36:19 CDT)
  1. smime.p7s (1764 bytes)
• Re: Steered MD with NAMD? Vincent Kraeutler (Thu Aug 02 2007 - 14:47:06 CDT)
  1. signature.asc (250 bytes)
• Re: Can NAMD be used as for general Newtonian mechanics simulations? Vincent Kraeutler (Sat Jul 28 2007 - 07:11:27 CDT)
  1. signature.asc (250 bytes)
• Re: Question regarding NAMD nonbonded routines Vincent Kraeutler (Fri Jul 27 2007 - 12:57:28 CDT)
  1. signature.asc (250 bytes)
• Re: Help Needed>Compiling source namd mpi enabled for a linux cluster Vincent Kraeutler (Fri Jul 27 2007 - 03:47:40 CDT)
  1. signature.asc (250 bytes)
• Re: Question regarding NAMD nonbonded routines Vincent Kraeutler (Thu Jul 26 2007 - 12:27:29 CDT)
  1. signature.asc (250 bytes)
• Question regarding NAMD nonbonded routines Vincent Kraeutler (Wed Jul 25 2007 - 11:55:40 CDT)
  1. signature.asc (250 bytes)
• A serious problem of NAMD output. Wang, Boyang (Tue Jul 24 2007 - 17:35:08 CDT)
  1. rotlectr0.psf (424 bytes)
• Re: ATP molecule snoze pa (Thu Jul 19 2007 - 12:40:35 CDT)
  1. ATP.pdb (5022 bytes)
• Restarting calculation missmatches Alexandre A. Vakhrouchev (Thu Jul 19 2007 - 00:59:36 CDT)
  1. vz_avg.png (4590 bytes)
• Re: removing waters from big dcd files Dong Luo (Mon Jul 16 2007 - 23:00:25 CDT)
  1. DCDframe.zip (20082 bytes)
• balck box: what is the coupling constant when using langenvinFile? Philipp Schön (Fri Jul 13 2007 - 06:53:38 CDT)
  1. smime.p7s (1764 bytes)
• TCL: force not a vector Peter Jones (Tue Jul 10 2007 - 21:39:04 CDT)
  1. tcl_forces_E (3276 bytes)
• Problems with using multiple Tclforces scripts sequentially maria goranovic (Tue Jul 10 2007 - 12:46:48 CDT)
  1. cons196.tcl (1600 bytes)
• can i somehow use reassigntemp for selected atoms only? Philipp Schön (Tue Jul 10 2007 - 11:06:51 CDT)
  1. smime.p7s (1764 bytes)
• Did anybody really use TIP4P? Alessio Alexiadis (Mon Jul 09 2007 - 09:52:47 CDT)
  1. TIP4P.zip (2608 bytes)
• Re: Re: Installing NAMD 2.6 on SMP machine... charm++ install errors Claudio Redaelli (Fri Jul 06 2007 - 04:14:39 CDT)
  1. LINUX_PWR5.tar.gz (2606 bytes)
• Re: ABF restrain alex digenova bravo (Thu Jul 05 2007 - 11:48:12 CDT)
  1. ABF.dat (5959 bytes)
• Re: Count protein solvent HBs? Dong Luo (Thu Jul 05 2007 - 09:21:36 CDT)
  1. hbonds.tcl (20260 bytes)
• problem with periodic boundaries Philipp Schön (Tue Jul 03 2007 - 10:13:04 CDT)
  1. smime.p7s (1764 bytes)
• Re: Changing loop to helix: restraining about 20 dihedral angles Jerome Henin (Sun Jun 24 2007 - 11:37:53 CDT)
  1. dummy.tcl (287 bytes)
• negative force shivam ghosh (Fri Jun 22 2007 - 00:42:24 CDT)
  1. ft_min0.pdf (7665 bytes)
• namd-l-outgoing2@halifax.ks.uiuc.edu sanghyuk_at_ewha.ac.kr (Wed Jun 20 2007 - 12:03:59 CDT)
  1. attachment.zip (1352 bytes)
• Re: Re: heat diffusion calculation QJos=E9_R=2E_Sabino=22?= (Mon Jun 18 2007 - 14:11:17 CDT)
  1. jrsabino.vcf (511 bytes)
• Re: Energy shift during simulation Cesar Luis Avila (Tue May 29 2007 - 09:53:31 CDT)
  1. energy.png (23524 bytes)
• basic pdb file run with namd and vmd Kayode Karunwi (Wed May 23 2007 - 16:05:01 CDT)
  1. alanine.pdb (1139 bytes)
  2. alanine.pgn.txt (168 bytes)
  3. alanine2.pdb (1092 bytes)
  4. alanine2.psf (3169 bytes)
  5. alanine2_wb.pdb (17412 bytes)
  6. alanine2_ws.pdb (1092 bytes)
  7. wat_sphere_alanine.tcl.txt (2089 bytes)
• Minimization Rita Cassia (Wed May 16 2007 - 12:19:51 CDT)
  1. ind.conf (4874 bytes)
• Re: how to use measure hbonds to calculate occupancy of all hbonds in simulation? lnubiofox (Wed May 16 2007 - 09:57:51 CDT)
  1. hbondoccupancy.txt (1148 bytes)
• Re: how to use measure hbonds to calculate occupancy of all hbonds in simulation? Dong Luo (Tue May 15 2007 - 18:27:01 CDT)
  1. hbond.tcl (2269 bytes)
• Re: files for air Jeffrey J. Potoff (Fri May 11 2007 - 07:21:20 CDT)
  1. h2s.pdb (270 bytes)
  2. build.tcl (132 bytes)
• Re: query about wrapped coordinates Gianluca Interlandi (Fri May 04 2007 - 14:54:20 CDT)
  1. DOC_unwrap.html (1140 bytes)
  2. unwrap.tcl (4957 bytes)
• abrupt deviation in rmsd values Monika Sharma (Wed May 02 2007 - 10:35:38 CDT)
  1. rmsd.dat (9927 bytes)
• Re: dcd binary file format Jeffrey A Tibbitt (Tue May 01 2007 - 16:57:47 CDT)
  1. syspart_dcd2 (6668 bytes)
• Re: Pressure Discrepancy Morad Alawneh (Fri Apr 20 2007 - 12:30:37 CDT)
  1. acf_pressure.pdf (2827 bytes)
• Re: Pressure Discrepancy Morad Alawneh (Fri Apr 20 2007 - 10:56:07 CDT)
  1. acf_pressure.pdf (22361 bytes)
• Re: Pressure Discrepancy Morad Alawneh (Tue Apr 03 2007 - 11:39:08 CDT)
  1. acf_pressure.pdf (17244 bytes)
• It doesn't work with using amber files. Hidekazu WATANABE (Thu Mar 29 2007 - 07:09:25 CDT)
  1. r800.new.pdb (3641 bytes)
• Help !!! ERROR: Atoms mooving too fast Juan Diaz (Tue Mar 27 2007 - 18:21:05 CDT)
  1. eq_npt_8.txt (3320 bytes)
• Re: Simulation explodes as soon as minimization starts "GRADIENT TOLERANCE: nan" namd vmd (Thu Mar 22 2007 - 07:55:00 CDT)
  1. top.inp.inp (929 bytes)
• Premature stop paco ty (Thu Mar 08 2007 - 03:57:15 CST)
  1. logfile.txt (7131 bytes)
• RDF.tcl question Jianhui Tian (Wed Feb 21 2007 - 12:43:24 CST)
  1. RDF.tcl (10381 bytes)
• Temperature problem Al-Rawi, Ahlam (Tue Feb 13 2007 - 14:05:35 CST)
  1. equ1.conf (1602 bytes)
• RE: DMPC psf. Lea Thøgersen (Fri Feb 09 2007 - 16:33:01 CST)
  1. DMPC.pdbalias (1281 bytes)
• "atoms moving too fast" error in bilayer simulation Himanshu Khandelia (Fri Feb 02 2007 - 07:31:53 CST)
  1. pope.in (1688 bytes)
• minimizing bad system: bad global excl. count Himanshu Khandelia (Tue Jan 23 2007 - 11:32:41 CST)
  1. config.in (1548 bytes)
• Stray PME grid charges detected Simon Watson (Tue Jan 09 2007 - 12:06:53 CST)
  1. eq0.conf (1234 bytes)

Last message date: Wed Dec 31 2008 - 05:25:21 CST
Archived on: Wed Feb 29 2012 - 15:48:55 CST

3952 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive