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NAMD-L: By messages with attachments

Search NAMD-L:

By messages with attachments

7959 messages sorted by: [ author ] [ date ] [ thread ] [ subject ]
About this archive

Starting: Mon Sep 08 2003 - 09:54:14 CDT
Ending: Fri Jul 04 2008 - 12:24:54 CDT

• 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)
• Simulating the orientation of detergent and lipid molecules around a membrane protein, bacteriorhodopsin Nathan H. Cho (Wed Dec 20 2006 - 20:59:20 CST)
  1. CHAPSO_H.pdb (8304 bytes)
• Is it equilibrated? taojinwuhan_at_sohu.com (Mon Dec 04 2006 - 01:45:49 CST)
  1. _____Microsoft_Word_____.doc (41472 bytes)
• error message in free energy pert. OMAR NABEEL ALY DEMERDASH (Sun Nov 26 2006 - 23:36:23 CST)
  1. 2eck_chrmv157_fep.conf (3179 bytes)
• LINE=*CMAP* regafan_at_usc.es (Wed Nov 22 2006 - 08:32:24 CST)
  1. min.log.gz (1221 bytes)
• ABF (fwd) Matthew Davies (Tue Nov 14 2006 - 07:40:30 CST)
  1. MHC_10_20.dat (2460 bytes)
  2. MHC_15_20.dat (1260 bytes)
• equilibration of protein Dhiraj Srivastava (Wed Nov 01 2006 - 12:31:17 CST)
  1. RMSD.doc (34816 bytes)
• Question about ABF Gaurav Sharma (Wed Oct 25 2006 - 18:03:13 CDT)
  1. ABF.doc (31744 bytes)
• Re: Warnings of psfgen Vishal Kopardé (Wed Oct 25 2006 - 17:09:15 CDT)
  1. pastedGraphic.pdf (25458 bytes)
• Warnings of psfgen Vishal Kopardé (Wed Oct 25 2006 - 08:37:30 CDT)
  1. out2 (18463 bytes)
• Re: phi and psi dihedral restraints luca (Mon Oct 23 2006 - 15:07:25 CDT)
  1. esempio_tcl_force.txt (2184 bytes)
• Multiple tclForcesScript Morad Alawneh (Sat Oct 14 2006 - 14:53:28 CDT)
  1. cylindrical_restraint.tcl (5593 bytes)
  2. spherical_restraint.tcl (5398 bytes)
• Re: "wrapAll on" with a complex Jerome Henin (Thu Oct 05 2006 - 22:08:18 CDT)
  1. DOC_unwrap.html (1140 bytes)
  2. unwrap.tcl (4957 bytes)
• Re: DPPC.Pdb file needed Elsa S. Henriques (Tue Sep 05 2006 - 08:42:29 CDT)
  1. DPPC.crd (9254 bytes)
• DPPC.Pdb file needed Lechuga, Javier (Mon Sep 04 2006 - 11:27:49 CDT)
  1. DPPC.pdb (9102 bytes)
• Re: CoordinateTransformation Sting (Sun Sep 03 2006 - 20:17:21 CDT)
  1. align_axis.tcl.txt (496 bytes)
• questions regarding output data of an ABF simulation Anahita Tafvizi (Mon Aug 07 2006 - 15:27:34 CDT)
  1. cons-dir.namd (12984 bytes)
• Re: RDF.tcl griadi_at_utalca.cl (Fri Jul 28 2006 - 17:01:24 CDT)
  1. counting_waters.tcl (1199 bytes)
• simulation crashing with nan Jackie (Wed Jul 26 2006 - 08:49:56 CDT)
  1. Problem.doc (25088 bytes)
• Re: psfgen gets ATP chiral atoms wrong Peter Freddolino (Tue Jul 25 2006 - 10:44:11 CDT)
  1. fixed.tgz (2937 bytes)
• Re: Queries on patches, GDP-topology Leonardo Trabuco (Mon Jul 24 2006 - 14:20:17 CDT)
  1. top_gdp.rtf (2707 bytes)
• Angle 2, Where is the problem [IMPORTANT] linefinc (Mon Jun 19 2006 - 11:50:41 CDT)
  1. co2.zip (25033 bytes)
• Lipid bilayer center go away from center of system. ghg_at_xalt.am (Sun Jun 18 2006 - 10:10:38 CDT)
  1. NPT.conf (3364 bytes)
• RE: Factorization in PMEGridSize JC Gumbart (Wed Jun 07 2006 - 09:25:24 CDT)
  1. image001.gif (339 bytes)
• the patch between segments for multiple chains molecule. Moumita Maiti (Fri Jun 02 2006 - 12:14:58 CDT)
  1. 1kx5.pgn (1369 bytes)
• Large energy fluctuation Sting (Mon May 30 2005 - 21:44:44 CDT)
  1. minimize.int (1261 bytes)
• Large energy fluctuation Sting (Fri Apr 08 2005 - 07:09:07 CDT)
  1. minimize.int (1261 bytes)
• questions regrading ABF Jan Saam (Mon May 29 2006 - 10:47:48 CDT)
  1. alanine.dat (1711 bytes)
• LDB problem on Dual Atlon64 X2 Sebastian Wasilewski (Wed May 17 2006 - 17:07:17 CDT)
  1. smime.p7s (3122 bytes)
• Re: namd: adding water molecules Mgr. Lubos Vrbka (Fri May 12 2006 - 00:51:02 CDT)
  1. smime.p7s (2341 bytes)
• periodic cell too small genie lfs (Wed May 10 2006 - 04:48:44 CDT)
  1. second.namd (2067 bytes)
  2. third.namd (2042 bytes)
  3. fourth.namd (2013 bytes)
• Re: why pressure is fluctuating so much Mgr. Lubos Vrbka (Fri Apr 28 2006 - 00:40:45 CDT)
  1. smime.p7s (2341 bytes)
• scaling NAMD2.6B1 on IBM P5 Thomas C. Bishop (Tue Apr 25 2006 - 14:44:33 CDT)
  1. dyn.NN.conf (2233 bytes)
• error related to tcl boundary forces gbellesia_at_chem.ucsb.edu (Tue Apr 25 2006 - 00:52:38 CDT)
  1. kffe.conf (2726 bytes)
• Re: NAMD-L: question about harmonic constraints JC Gumbart (Tue Apr 11 2006 - 17:41:08 CDT)
  1. cv_deca.tcl (2165 bytes)
• error about tclForcesScript xiaojing gong (Mon Apr 10 2006 - 09:21:13 CDT)
  1. min_2.log (3130 bytes)
• parameter file for DAD Yu Wang (Fri Apr 07 2006 - 09:18:55 CDT)
  1. wy0519.vcf (268 bytes)
• Simulation failed during the stage of heat Shulin Zhuang (Thu Mar 23 2006 - 23:58:15 CST)
  1. heating.namd (2255 bytes)
• Re: area per lipid for a protein embedded membrane system Nicolas Sapay (Sat Mar 11 2006 - 04:42:32 CST)
  1. area.tar.gz (6398 bytes)
• Re: Aligning structures Peter Freddolino (Thu Mar 09 2006 - 21:37:05 CST)
  1. align_frames.tcl (409 bytes)
• Re: Spherical harmonic restraint Morad Alawneh (Thu Mar 02 2006 - 13:25:39 CST)
  1. keep_water_out.tcl (7636 bytes)
• question on membrane crushing Longzhu Shen (Thu Mar 02 2006 - 15:18:09 CST)
  1. eqmd.in (2610 bytes)
• Re: Alchemical Free Energy Perturbation jsachs_at_mail.csb.yale.edu (Wed Mar 01 2006 - 15:31:07 CST)
  1. asa_dual.pdb (3076 bytes)
  2. asa_alchemify.psf (10667 bytes)
  3. fep.namd (1538 bytes)
• Alchemical Free Energy Perturbation Jawahar Neelankatan (Sat Feb 25 2006 - 00:40:02 CST)
  1. fep.conf (1779 bytes)
  2. ion.fep (214 bytes)
• Alchemical Free Energy Perturbation Jawahar Neelankatan (Sat Feb 25 2006 - 01:36:29 CST)
  1. fep.conf (1779 bytes)
  2. ion.fep (214 bytes)
• Free Cluster-Building Workshops - 16-17 Mar 2006, 20-21 Apr 2006 Tim Skirvin (Mon Feb 13 2006 - 14:41:24 CST)
  1. part (186 bytes)
• Fwd: Water Box size snoze pa (Fri Feb 10 2006 - 10:58:27 CST)
  1. namdmin.png (90535 bytes)
  2. namd1ns.png (97173 bytes)
• pairInteractionSelf Yu Wang (Fri Feb 10 2006 - 03:19:34 CST)
  1. wy0519.vcf (268 bytes)
• Re: Saving coordinates of each frame into one separate .pdb file from a 100-frame .dcd file. Carlos Simoes (Sat Jan 21 2006 - 11:04:54 CST)
  1. splitmultiframepdb2files.tcl (781 bytes)
• Re: velocity error, still bo baker (Wed Jan 11 2006 - 16:20:37 CST)
  1. NPT2-011006.conf (1213 bytes)
  2. NPT3-011006.conf (1233 bytes)
• velocity error, still bo baker (Tue Jan 10 2006 - 15:20:58 CST)
  1. NPT1-011006.conf (1213 bytes)
• same random numbers?? Shahid Qamar (Fri Jan 06 2006 - 15:49:01 CST)
  1. random.txt (959 bytes)
• Re: velocity error bo baker (Thu Jan 05 2006 - 18:02:35 CST)
  1. NPT1.conf (1214 bytes)
  2. 4.log (9250 bytes)
• Re: Energy Plugin bo baker (Wed Jan 04 2006 - 16:26:24 CST)
  1. namdplot (3535 bytes)
  2. 2 (3662 bytes)
• velocity error bo baker (Wed Jan 04 2006 - 13:12:45 CST)
  1. 3.log (9853 bytes)
  2. NPT.conf (1385 bytes)
• FATAL ERROR: unknown floating-point error, errno = 4 Manori Indira Jayasinghe (Thu Dec 22 2005 - 23:16:41 CST)
  1. md_zero.namd (3685 bytes)
• Re: define abf1 and abf2 for CM of water and CM of molecule Manori Indira Jayasinghe (Wed Dec 21 2005 - 11:26:37 CST)
  1. md_zero.namd (3680 bytes)
• Errors: Periodic cell became too small for original patch grid & Setting parameter binaryoutput from script failed! Nitin Bhardwaj (Sun Nov 13 2005 - 12:26:35 CST)
  1. popc_s.conf (1703 bytes)
• Re: ABF Simulation Jérôme Hénin (Fri Oct 28 2005 - 04:05:52 CDT)
  1. vectors.tcl (10343 bytes)
• scaling issue Robert Bjornson (Fri Oct 21 2005 - 15:56:13 CDT)
  1. prod2.namd (2773 bytes)
  2. apoa1.namd (851 bytes)
• Re: namdplot: command not found Robert Brunner (Thu Oct 13 2005 - 15:11:37 CDT)
  1. smime.p7s (2363 bytes)
  2. PGP.sig (187 bytes)
• Re: namdplot: command not found bo baker (Tue Oct 11 2005 - 18:56:10 CDT)
  1. namdplot (3535 bytes)
• Re: namdplot: command not found Robert Brunner (Tue Oct 11 2005 - 10:32:00 CDT)
  1. smime.p7s (2363 bytes)
  2. PGP.sig (187 bytes)
• RE: autoionize & namd2 Michel Espinoza-Fonseca (Thu Sep 22 2005 - 02:51:08 CDT)
  1. test.in (1882 bytes)
• problem when heating the system Phoenix (Mon Aug 29 2005 - 23:07:42 CDT)
  1. heat.cfg (1198 bytes)
• ERROR: Margin is too small (BUG?) Mauricio Carrillo Tripp (Wed Aug 03 2005 - 10:02:42 CDT)
  1. mini-heat.namd (2288 bytes)
• Re: Report on a trajectory incompatibility between NAMD and CHARMM: Unfolding and RDFs NAVEEN P MICHAUD AGRAWAL (Fri Jul 29 2005 - 23:30:23 CDT)
  1. dcdcellfix.tar (102400 bytes)
• Velocity after heating mustapha.hamdi_at_ensi-bourges.fr (Mon Jul 18 2005 - 06:56:03 CDT)
  1. position_restrained.log (13533 bytes)
• Re: Runnig same config file many times Mauricio Carrillo Tripp (Fri Jul 15 2005 - 17:33:48 CDT)
  1. namd.csh (513 bytes)
• RE: Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints ) JC Gumbart (Wed Jun 29 2005 - 11:18:23 CDT)
  1. keep_water_out.tcl (7635 bytes)
• Re: catdcd and dcdunitcell Jérôme Hénin (Tue Jun 28 2005 - 09:14:32 CDT)
  1. catdcd.gz (12558 bytes)
• autoimd on windows Anna Modzelewska (Mon Jun 20 2005 - 06:40:29 CDT)
  1. autoimd.log (2741 bytes)
• How to conservate energy during NVE simulations??? Leonardo Sepulveda Durán (Wed Jun 15 2005 - 20:55:29 CDT)
  1. equil_data1_TempPresTotEn.pdf (48858 bytes)
• Re: Multiple Harmonic Constraints Sascha Tayefeh (Thu Jun 09 2005 - 08:28:52 CDT)
  1. sascha.vcf (372 bytes)
• Multiple Harmonic Constraints Sascha Tayefeh (Thu Jun 09 2005 - 02:31:38 CDT)
  1. sascha.vcf (372 bytes)
• config files Mark A. Hallman (Tue Jun 07 2005 - 12:17:35 CDT)
  1. minimize.namd (882 bytes)
• Re: NADP problem Hemant Kushwaha (Fri Jun 03 2005 - 22:07:08 CDT)
  1. nadp.top (11769 bytes)
• Re: NADP problem Hemant Kushwaha (Fri Jun 03 2005 - 08:28:56 CDT)
  1. nadp.top (11768 bytes)
• about *.psf ËïæÃæà(Thu May 26 2005 - 23:59:07 CDT)
  1. lig1.gif (3592 bytes)
• Re: Re: Simulated Annealing Config Leonardo Sepulveda Durán (Tue May 24 2005 - 14:55:49 CDT)
  1. ubq.conf (3346 bytes)
• What's wrong with my namd2 Xiaoqing Wang (Sun May 15 2005 - 07:01:13 CDT)
  1. 8 (959438 bytes)
• Re: Leandro Martínez (Fri Apr 08 2005 - 13:50:34 CDT)
  1. atomnames.f (3102 bytes)
• Re: NMAD job abnormally killed with PBS Chris Samuel (Wed Apr 06 2005 - 22:32:01 CDT)
  1. part (190 bytes)
• Re: FATAL ERROR: Stale NFS file handle Chris Samuel (Wed Apr 06 2005 - 22:29:59 CDT)
  1. part (190 bytes)
• RATTLE and DNA Nicholas M Glykos (Tue Apr 05 2005 - 05:33:48 CDT)
  1. heat.namd (3877 bytes)
  2. equi.namd (2125 bytes)
• Re: problem running namd Chris Samuel (Mon Apr 04 2005 - 18:10:58 CDT)
  1. part (190 bytes)
• Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Chris Samuel (Wed Mar 30 2005 - 00:05:44 CST)
  1. part (190 bytes)
• Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Chris Samuel (Sun Mar 20 2005 - 20:04:50 CST)
  1. part (190 bytes)
• Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Chris Samuel (Thu Mar 17 2005 - 23:23:24 CST)
  1. part (190 bytes)
• Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Chris Samuel (Wed Mar 16 2005 - 00:06:21 CST)
  1. part (190 bytes)
• Re: G5 clusters Gengbin Zheng (Tue Mar 08 2005 - 12:44:25 CST)
  1. apoa1_bench.png (12517 bytes)
• Re: segmentation violation!! Robert Brunner (Tue Jan 18 2005 - 11:05:00 CST)
  1. PGP.sig (187 bytes)
• multiple jobs on a cluster Cheri M Turman (Wed Jan 12 2005 - 15:55:42 CST)
  1. cturman.vcf (336 bytes)
• about MCTI output mashaojie163 (Mon Dec 27 2004 - 01:29:36 CST)
  1. clip_image002.gif (168 bytes)
  2. clip_image002.gif (315 bytes)
  3. clip_image002.gif (168 bytes)
  4. clip_image002.gif (147 bytes)
• FATAL ERROR: Asymmetric water molecule ? Gaurav Sharma (Tue Dec 21 2004 - 14:58:11 CST)
  1. output.log (3898 bytes)
• Re: How I can run two simulations one after an other Michael Grabe (Tue Dec 14 2004 - 15:15:36 CST)
  1. md_script (841 bytes)
  2. fep_script (665 bytes)
• Re: Variation of results in iterations Robert Brunner (Mon Dec 06 2004 - 21:15:00 CST)
  1. PGP.sig (187 bytes)
• Re: NAMD on Xeon EM64T Chris Samuel (Thu Dec 02 2004 - 22:18:39 CST)
  1. part (190 bytes)
• Re: NAMD Source Robert Brunner (Fri Nov 19 2004 - 10:54:16 CST)
  1. PGP.sig (187 bytes)
• Rif: Re: Rif: Re: Rif: Re: Rif: Re: linux cluster trouble max (Fri Nov 19 2004 - 03:47:01 CST)
  1. IMSTP.gif (494 bytes)
  2. namd.out (27427 bytes)
• linux cluster trouble max (Tue Nov 16 2004 - 04:44:36 CST)
  1. IMSTP.gif (494 bytes)
• Rif: Re: linux cluster trouble max (Wed Nov 10 2004 - 03:00:42 CST)
  1. IMSTP.gif (494 bytes)
• Re: Sample Configuratiion files Cheri M Turman (Wed Nov 03 2004 - 19:47:25 CST)
  1. cturman.vcf (336 bytes)
• Re: System minimization: fail after 199 steps Charles Danko (Wed Nov 03 2004 - 11:53:06 CST)
  1. minimize.namd (2698 bytes)
• Tcl dihedral restraints in CG minimisation Ben Roberts (Tue Nov 02 2004 - 17:01:28 CST)
  1. restraints.tcl (13840 bytes)
• Re: [Periodic Boundary]: from charmm to namd Sascha Tayefeh (Tue Nov 02 2004 - 12:46:02 CST)
  1. sascha.vcf (397 bytes)
• [Periodic Boundary]: from charmm to namd Sascha Tayefeh (Tue Nov 02 2004 - 09:08:42 CST)
  1. sascha.vcf (397 bytes)
• HEM residue in NAMD Peter Bazeley (Tue Nov 02 2004 - 02:23:50 CST)
  1. 2D6H_fixed_heme_bak.pdb (6068 bytes)
• FK506 ligand topology file(1FKF) MERIC AYSE OVACIK (Thu Oct 28 2004 - 05:29:21 CDT)
  1. part (824 bytes)
• Re: Compilation on an Opteron Server SuSE Linux Enterprise System Version 8 Chris Samuel (Wed Oct 20 2004 - 18:05:49 CDT)
  1. part (190 bytes)
• Re: NAMD on Linux cluster with Myrinet Chris Samuel (Mon Oct 18 2004 - 23:02:27 CDT)
  1. part (190 bytes)
• bug report and stray pme Cheri M Turman (Mon Oct 18 2004 - 16:23:42 CDT)
  1. cturman.vcf (336 bytes)
• [Fwd: counterion software] Cetin Baloglu (Sun Oct 10 2004 - 23:55:20 CDT)
  1. cetinb.vcf (342 bytes)
• counterion software Cetin Baloglu (Sun Oct 10 2004 - 23:51:56 CDT)
  1. cetinb.vcf (342 bytes)
• Fw: Constraint failure in RATTLE algorithm Zhong Wenyu (Sun Sep 19 2004 - 02:14:27 CDT)
  1. open4.namd (2190 bytes)
  2. open4.log (19290 bytes)
• Re: Compilation on Opteron Chris Samuel (Thu Aug 26 2004 - 00:04:07 CDT)
  1. part (190 bytes)
• RE: radial distribution function Liu, Zhanwu (Fri Aug 13 2004 - 08:40:51 CDT)
  1. RDF.tcl (10381 bytes)
• Re: Need to add Hydrogens to over 300 distinct PDB's Edward Patrick Obrien (Wed Aug 11 2004 - 13:05:33 CDT)
  1. Add_Atoms_to_PDBs.pl (3307 bytes)
• HYP files Ivan Vinogradov (Tue Aug 03 2004 - 12:55:52 CDT)
  1. top_hyp.inp (2006 bytes)
  2. par_hyp.inp (351 bytes)
• charm++ MPICH and Myrinet Mauricio Carrillo Tripp (Mon Jul 26 2004 - 17:34:53 CDT)
  1. 01.log (11715 bytes)
• Warning: Not all atoms have unique coordinates. Shirley Hui (Thu Jul 08 2004 - 09:25:13 CDT)
  1. cpc.conf (2926 bytes)
• Re: icc compilation problem Chris Samuel (Sun Jul 04 2004 - 20:41:14 CDT)
  1. part (190 bytes)
• Re: icc compilation problem Chris Samuel (Thu Jul 01 2004 - 18:11:57 CDT)
  1. part (190 bytes)
• pmf error mashaojie163 (Mon Jun 21 2004 - 10:17:20 CDT)
  1. pmf.conf (2407 bytes)
  2. run.log (700 bytes)
• Simulated Annealing Config Ahmet Bakan (Tue Jun 15 2004 - 08:24:59 CDT)
  1. SA.JPG (42098 bytes)
  2. namd.run (909 bytes)
• Re: Force Calculation in NAMD Gadi Oron (Sun May 23 2004 - 02:37:27 CDT)
  1. 8859-8 (2126 bytes)
• Why Vmd didn't show the Pt-Cl bond myang (Wed May 19 2004 - 18:46:31 CDT)
  1. K2PtCl6_less.pdb (1865 bytes)
• autoionize script amodzelewska_at_dns.iimcb.gov.pl (Sun May 16 2004 - 13:21:58 CDT)
  1. ions.top (1176 bytes)
• installing on beowulf cluster Cheri M Turman (Sun May 09 2004 - 19:58:25 CDT)
  1. cturman.vcf (336 bytes)
• installing on beowulf cluster Cheri M Turman (Thu May 06 2004 - 13:38:16 CDT)
  1. cturman.vcf (336 bytes)
• Re: ,log and .out files with namd running on mac os x (panther) Arieana Moore (Wed May 05 2004 - 17:30:28 CDT)
  1. cnt_mod3.out (5817 bytes)
  2. cnt_mod3.conf (2999 bytes)
• RE: Binding free energy of a protein complex Ahmet Bakan (Mon May 03 2004 - 06:02:29 CDT)
  1. hbond.tcl (3461 bytes)
• problems with namdplot fixed by using new plotting program Cheri M Turman (Tue Apr 27 2004 - 16:34:42 CDT)
  1. cturman.vcf (336 bytes)
• temperature question in logfile Cheri M Turman (Tue Apr 20 2004 - 17:13:28 CDT)
  1. cturman.vcf (336 bytes)
• Re: still problems with namdplot Gadi Oron (Sun Apr 18 2004 - 01:51:42 CDT)
  1. 8859-8 (3707 bytes)
  2. 8859-8 (3688 bytes)
• still problems with namdplot Cheri M Turman (Thu Apr 15 2004 - 14:13:57 CDT)
  1. cturman.vcf (336 bytes)
• Re: More NAMD/gm2 problems Chris Samuel (Wed Mar 31 2004 - 00:40:36 CST)
  1. charmc.patch (349 bytes)
  2. mpicc.h (200 bytes)
  3. mpicc.sh (538 bytes)
• A tool to set up alchemical FEP transformations Jérôme Hénin (Mon Mar 29 2004 - 10:27:12 CST)
  1. alchemify.tar.gz (20572 bytes)
• Re: CP3-NH3 error Tim Isgro (Thu Mar 04 2004 - 13:56:44 CST)
  1. HERGpsfgen.txt (508 bytes)
• Re: Minimization with CHARMM Tim Isgro (Mon Feb 09 2004 - 17:04:13 CST)
  1. sample.conf (4331 bytes)
• RE: minimization problem - "Bad global exclusion count,possible error!" Frances Leung (Fri Jan 30 2004 - 02:52:09 CST)
  1. psfgen_log.txt (52161 bytes)
• minimization problem - "Bad global exclusion count, possible error!" Frances Leung (Thu Jan 29 2004 - 19:25:27 CST)
  1. minimize_log.txt (15543 bytes)
• Parameters and topologies for aa at different protonation states Bartosz Dobrzelecki (Fri Jan 23 2004 - 06:45:26 CST)
  1. signature.asc (190 bytes)
• missing atoms warnings for psfgen Frances Leung (Mon Jan 19 2004 - 21:47:33 CST)
  1. psflog.txt (142065 bytes)
• Potential Terms AHMET BAKAN (Mon Jan 05 2004 - 12:20:02 CST)
  1. 2_Theory.fm.anc.gif (13045 bytes)
• alchemical free energy perturbation AMIT PALIWAL (Mon Jan 05 2004 - 00:37:05 CST)
  1. growth.namd (1866 bytes)
  2. system.fep (450 bytes)
• Simulating RNA+PROTEIN complexes Bartosz Dobrzelecki (Fri Dec 19 2003 - 14:30:23 CST)
  1. signature.asc (190 bytes)
• Re: Help! unstable simulation - ARG go nuts... Gadi Oron (Tue Dec 16 2003 - 09:33:25 CST)
  1. snap.png (53801 bytes)
• Re: Help! unstable simulation. Alexandre Vakhrouchev (Fri Dec 12 2003 - 03:16:55 CST)
  1. psf.log (5144 bytes)
• simulated annealing script Cheri M Turman (Thu Sep 25 2003 - 13:15:10 CDT)
  1. cturman.vcf (336 bytes)
• Re: Re: seg fault and namdplot problem Cheri M Turman (Mon Sep 22 2003 - 18:58:30 CDT)
  1. cturman.vcf (336 bytes)
• Re: seg fault and namdplot problem Cheri M Turman (Mon Sep 22 2003 - 16:22:46 CDT)
  1. cturman.vcf (336 bytes)
• segmentation fault Cheri M Turman (Tue Sep 16 2003 - 14:12:43 CDT)
  1. W1A1_wb.log (15255 bytes)
  2. cturman.vcf (336 bytes)

Last message date: Fri Jul 04 2008 - 12:24:54 CDT
Archived on: Fri Jul 04 2008 - 19:18:31 CDT

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Beckman Institute for Advanced Science and Technology // National Institutes of Health // National Science Foundation // Physics, Computer Science, and Biophysics at UIUC
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