NAMD-L: By messages with attachments
By messages with attachments
11114 messages sorted by:
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About this archive
Starting: Mon Sep 08 2003 - 09:54:14 CDT
Ending: Sat Nov 07 2009 - 03:09:56 CST
- Re: ibverbs crash Bjoern Olausson (Wed Nov 04 2009 - 08:38:25 CST)
- ibverbs.c (92079 bytes)
- signature.asc_ (199 bytes)
- Re: ibverbs crash Bjoern Olausson (Wed Nov 04 2009 - 04:06:48 CST)
- signature.asc_ (199 bytes)
- Re: ibverbs crash Bjoern Olausson (Wed Nov 04 2009 - 08:38:45 CST)
- signature.asc_ (199 bytes)
- issues with AutoPSF for a cyclodextrin CHINDEA Vlad (Thu Oct 29 2009 - 18:32:50 CDT)
- amidon4.pdb (16877 bytes)
- Re: Fullerene topology Luca Muccioli (Wed Oct 28 2009 - 10:55:11 CDT)
- About NAN error cong chen (Fri Sep 18 2009 - 01:35:51 CDT)
- water-10-npt.log (2175362 bytes)
- water-10-npt.conf (3439 bytes)
- Re: Regarding ABF Simulation Jagan Mohan (Tue Sep 15 2009 - 00:10:48 CDT)
- eqf_inp_back (2020 bytes)
- Re: Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? Bjoern Olausson (Thu Sep 10 2009 - 05:38:18 CDT)
- signature.asc_ (199 bytes)
- Re: Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? Bjoern Olausson (Thu Sep 10 2009 - 05:26:00 CDT)
- signature.asc_ (199 bytes)
- Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? Bjoern Olausson (Tue Sep 08 2009 - 03:12:04 CDT)
- signature.asc_ (199 bytes)
- Constraint failure in RATTLE algorithm - shouldn't a rerun fail at the same step? Bjoern Olausson (Tue Sep 08 2009 - 03:13:02 CDT)
- signature.asc_ (199 bytes)
- Re-posting - Methylated Histidine topology file Sujata Sovani (Mon Aug 31 2009 - 12:47:16 CDT)
- MeHIS2.doc (24064 bytes)
- Methylated Histidine topology file Sujata Sovani (Mon Aug 31 2009 - 12:38:03 CDT)
- MeHIS2.doc (24064 bytes)
- hole on the surface of the waterbox Mert Gür (Fri Aug 28 2009 - 05:08:09 CDT)
- molcom.conf (1599 bytes)
- Postdoc position in biomolecular simulation Ivaylo Ivanov (Wed Aug 26 2009 - 16:40:02 CDT)
- positions.pdf (11803 bytes)
- Re: charm++ how to handle SMP/Multicore Bjoern Olausson (Thu Aug 20 2009 - 11:41:16 CDT)
- signature.asc_ (199 bytes)
- restating simuation and periodic cell conditions gurunath katagi (Tue Aug 18 2009 - 03:23:20 CDT)
- protein.conf (3955 bytes)
- Re: Error with GUI NAMD Energy snoze pa (Mon Aug 10 2009 - 11:32:53 CDT)
- namdlog.pl (924 bytes)
- FEP implementation in NAMD 2.6 vs. 2.7b1 Dan Bolintineanu (Tue Jul 28 2009 - 16:50:37 CDT)
- ethane3.namd (2350 bytes)
- NAMD 2.7b1 with APBS/iAPBS Bjoern Olausson (Wed Jul 22 2009 - 02:56:07 CDT)
- signature.asc_ (199 bytes)
- Minimization problem of a protein-DNA complex with namd sudipta (Sun Jul 12 2009 - 02:21:36 CDT)
- pro_dna_new_cc.in (5103 bytes)
- pro_dna_minimization.conf (2790 bytes)
- Re: Value for "firsttimestep" when restarting MD Bjoern Olausson (Thu Jul 02 2009 - 04:05:23 CDT)
- signature.asc_ (199 bytes)
- RE: ABF simulations Branko (Tue Jun 23 2009 - 14:52:42 CDT)
- Example.tif (13176 bytes)
- Postdoc position in biomolecular simulation Ivaylo, Ivanov (Sat Jun 13 2009 - 02:08:07 CDT)
- positions.pdf (21058 bytes)
- Postdoc position in biomolecular simulation Ivaylo, Ivanov (Sat Jun 13 2009 - 01:37:55 CDT)
- positions.pdf (21058 bytes)
- FATAL ERROR: Bad global exclusion count! KIRTANA S (Mon Jun 01 2009 - 12:37:38 CDT)
- parameter.rtf (2239 bytes)
- psf.rtf (7629 bytes)
- regd: my parameter file KIRTANA S (Fri May 29 2009 - 16:05:26 CDT)
- par_all27_prot_lipid.inp (759 bytes)
- psf.rtf (7629 bytes)
- Re: water tail correction Floris Buelens (Fri May 22 2009 - 05:40:00 CDT)
- LJcorrection.diff (5368 bytes)
- LJcorrection_validation.txt (6002 bytes)
- Need help to generate ubq-get-energy.conf Mert Gür (Wed May 13 2009 - 10:06:55 CDT)
- 1EJG.conf (1674 bytes)
- Re: Make NAMD2.7b1 with cuda bug? Axel Kohlmeyer (Wed May 13 2009 - 10:03:44 CDT)
- back_end.diff.gz (455 bytes)
- Which compiler-suite was used... Bjoern Olausson (Tue May 12 2009 - 07:26:00 CDT)
- signature.asc_ (199 bytes)
- Re: Value for "firsttimestep" when restarting MD Bjoern Olausson (Tue May 05 2009 - 12:45:56 CDT)
- signature.asc_ (199 bytes)
- Re: dummy atom mass changed yun luo (Tue May 05 2009 - 12:19:05 CDT)
- memb2_fep.png (7043 bytes)
- Re: dummy atom mass changed Jerome Henin (Tue May 05 2009 - 10:43:48 CDT)
- lambda.png (16558 bytes)
- Value for "firsttimestep" when restarting MD Bjoern Olausson (Tue May 05 2009 - 09:50:42 CDT)
- signature.asc_ (199 bytes)
- regarding simulation prasun kumar (Tue May 05 2009 - 08:48:00 CDT)
- dna1.conf (3202 bytes)
- structure problem Ahlam Al-Rawi (Wed Apr 22 2009 - 12:22:29 CDT)
- corey.pdb (23316 bytes)
- Re: Unfavorable anti conformation after GLUP patching? Sebastian Stolzenberg (Thu Apr 16 2009 - 11:00:17 CDT)
- pmf.tcl (224 bytes)
- Re: how to do: FEP e2?, a protonating mutation? Sébastien Légaré (Thu Apr 09 2009 - 10:48:06 CDT)
- glud1.txt (3053 bytes)
- how to do: FEP e2?, a protonating mutation? Sebastian Stolzenberg (Tue Apr 07 2009 - 19:15:19 CDT)
- GLU2GLUP.pdf (25541 bytes)
- About CUDA version of NAMD 2.7 B1 wang (Wed Mar 25 2009 - 00:57:33 CDT)
- c00jsw00.vcf (879 bytes)
- acridine orange Rudra Banerjee (Thu Mar 19 2009 - 23:54:50 CDT)
- ao.pdf (4692 bytes)
- Re: Reference file for the constraining force in Umbrella Sampling Mert Gür (Sat Mar 14 2009 - 07:10:35 CDT)
- molcom.conf (4009 bytes)
- Re: topology and parameter file for FAD Schreiner Eduard (Sun Mar 01 2009 - 01:52:09 CST)
- Dagger.gif (105 bytes)
- Dagger.gif (105 bytes)
- Re: cgmd stability wang (Wed Feb 25 2009 - 21:43:41 CST)
- c00jsw00.vcf (879 bytes)
- Re: cgmd stability wang (Mon Feb 23 2009 - 23:49:47 CST)
- c00jsw00.vcf (864 bytes)
- RE: Autopsf error with a modified top file CHINDEA Vlad (Fri Feb 20 2009 - 19:28:28 CST)
- para.pdb (1585 bytes)
- (no subject) gurunath katagi (Fri Feb 20 2009 - 06:08:37 CST)
- sample.txt (8722 bytes)
- protein.conf (3925 bytes)
- Re: cgmd stability wang (Thu Feb 19 2009 - 03:15:56 CST)
- c00jsw00.vcf (879 bytes)
- Autopsf error with a modified top file CHINDEA Vlad (Wed Feb 18 2009 - 15:17:52 CST)
- top_para.inp (10344 bytes)
- tcl script fett_at_vtr.net (Mon Feb 02 2009 - 21:31:04 CST)
- kineticv2.tcl (3299 bytes)
- (no subject) OZGE ENGIN (Wed Jan 28 2009 - 03:29:03 CST)
- udp.psf (14881 bytes)
- Re: Inorganic compounds Chris Harrison (Wed Jan 14 2009 - 23:25:19 CST)
- image002.jpg (3133 bytes)
- Inorganic compounds Casey,Richard (Thu Jan 08 2009 - 12:20:34 CST)
- image002.jpg (3133 bytes)
- 4.jpg (30468 bytes)
- Re: namdcvs Achani.K.Yatawara_at_Dartmouth.edu (Mon Jan 05 2009 - 13:32:34 CST)
- massage (17679 bytes)
- Re: namd cvs compilation BIN ZHANG (Mon Dec 01 2008 - 11:59:39 CST)
- 1.conf (2321 bytes)
- H-bond occupancy in nucleic acids Tianjiao Wang (Thu Nov 20 2008 - 10:08:27 CST)
- hbonds.tcl (20260 bytes)
- ABF:problems with calculating Free Energy Profile supram_at_nankai.edu.cn (Sun Nov 16 2008 - 20:55:39 CST)
- bcdlglu.abf (14219 bytes)
- NAMD Simulation error Anirban Ghosh (Fri Nov 14 2008 - 02:36:16 CST)
- CG.conf (2737 bytes)
- NAMD Simulation error Anirban Ghosh (Wed Nov 12 2008 - 22:41:07 CST)
- 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)
- ser39ala_wb_mn.xst (2047 bytes)
- ser39ala_wb_eq.xst (172 bytes)
- Re: ABF - using gyration Jerome Henin (Tue Oct 28 2008 - 15:11:43 CDT)
- abf_script.tcl (21731 bytes)
- gyration.tcl (2758 bytes)
- ABF backbone dihedral Sébastien Légaré (Tue Oct 28 2008 - 11:44:21 CDT)
- helix.tcl (8212 bytes)
- Backbone dihedral ABF Sébastien Légaré (Tue Oct 28 2008 - 11:50:02 CDT)
- 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)
- 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)
- pyramida.top (317 bytes)
- FW: psf generation for a small non-peptide molecule - again CHINDEA Vlad (Mon Sep 29 2008 - 17:21:16 CDT)
- azi.pdb (11017 bytes)
- unk_azi.xbgf (1974 bytes)
- Namd water density jouko_at_uchicago.edu (Mon Sep 22 2008 - 21:36:11 CDT)
- bakforeq.conf.md (4458 bytes)
- Re: need help on CG modelling Nicolas Sapay (Mon Sep 22 2008 - 13:59:16 CDT)
- nsapay.vcf (283 bytes)
- Re: need help on CG modelling Nicolas Sapay (Mon Sep 22 2008 - 12:34:47 CDT)
- nsapay.vcf (283 bytes)
- TCL Forces : OUT OF MEMORY BIN ZHANG (Fri Sep 12 2008 - 13:38:17 CDT)
- derv.tcl (6532 bytes)
- wham_1d.tcl (2613 bytes)
- NAMD compilation / TACC Ranger Arturas Ziemys (Thu Aug 28 2008 - 11:25:14 CDT)
- Ranger-2.log.gz (5595 bytes)
- Re: How to write gradual heating config file Hyundeok Song (Mon Aug 25 2008 - 19:30:26 CDT)
- heat7.ps (14452 bytes)
- Re: unwanted bonds in .pdb file while using molefacture Subhashis Biswas (Wed Aug 06 2008 - 14:23:23 CDT)
- GCTiO2.pdb (9872 bytes)
- Constraining center of mass of monomers S.K. Ghosh (Wed Jul 16 2008 - 17:45:57 CDT)
- smd.tcl (1548 bytes)
- memory overflow problem of Tcl scripting when dealing with trajectories bo liu (Wed Jul 16 2008 - 03:16:31 CDT)
- dipole_profile.tcl (6794 bytes)
- Re: Rise in Total Energy in NVE S.K. Ghosh (Wed Jul 09 2008 - 10:25:35 CDT)
- 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)
- 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)
- hbonds.tcl (20260 bytes)
- hbonds1.txt (4685 bytes)
- hbonds2.txt (2876 bytes)
- Bond energy become Zero!!! Ming (Thu Jun 05 2008 - 04:17:01 CDT)
- CH4.top (2802 bytes)
- CH4.par (4084 bytes)
- CH4_try.psf (1092 bytes)
- CH4_try.pdb (452 bytes)
- Re: The correct topology/parameter file and pgn S.K. Ghosh (Wed Jun 04 2008 - 13:48:41 CDT)
- 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)
- eF_water_test.conf (3874 bytes)
- Re: Error Parsing Config File MIke S (Mon May 26 2008 - 15:46:19 CDT)
- trial.conf (5718 bytes)
- Energy plot script Alexandre A. Vakhrouchev (Wed May 14 2008 - 22:11:19 CDT)
- plot_energy.sh.gz (1205 bytes)
- What does "cellOrigin" really mean? bo liu (Wed Apr 23 2008 - 05:48:45 CDT)
- pic1.JPG (21336 bytes)
- What does "cellOrigin" really mean? bo liu (Fri Apr 18 2008 - 09:38:56 CDT)
- 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)
- fep.conf (2878 bytes)
- NAMD stops running without error messages or termination Yinglong Miao (Mon Mar 03 2008 - 17:18:12 CST)
- NAMD.tcl (1904 bytes)
- protein_RNA simulation sripad chandan (Sat Mar 01 2008 - 08:43:22 CST)
- xmin.conf (2396 bytes)
- comp.pgn.txt (703 bytes)
- namd_minimize sripad chandan (Sun Feb 24 2008 - 10:51:47 CST)
- 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)
- tyr2ala.pdb (4637 bytes)
- ABF question Matthew Davies (Wed Feb 13 2008 - 11:00:44 CST)
- abf.dat (660 bytes)
- Re: catDCD 32 bit Vs. 64 bit Version Philip Peartree (Thu Feb 07 2008 - 09:28:15 CST)
- 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)
- input-file.doc (26624 bytes)
- 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)
- mach.sh (939 bytes)
- Re: Segmentation violation when running without an internet connection Robert Brunner (Thu Dec 20 2007 - 14:45:41 CST)
- smime.p7s (2417 bytes)
- Re: problems replicating a DOPC membrane Richard Swenson (Thu Nov 29 2007 - 14:57:35 CST)
- cla_psf.tcl (383 bytes)
- dopc_psf.tcl (783 bytes)
- fix.tcl (1075 bytes)
- reformat.sh (951 bytes)
- sod_psf.tcl (379 bytes)
- system_psf.tcl (545 bytes)
- water_psf.tcl (520 bytes)
- Re: Is there solution to numerical inaccuracy Alok Juneja (Fri Nov 23 2007 - 12:14:01 CST)
- comparision.pdf (6353 bytes)
- B1-B2.pdf (2997 bytes)
- Re: Replica Exchange NAMD John R. Dowdle (Mon Nov 19 2007 - 20:16:43 CST)
- signature.asc (190 bytes)
- heat flux when using langevin dynamics Philipp Schön (Thu Nov 01 2007 - 09:12:56 CDT)
- smime.p7s (1764 bytes)
- Errors during equilibration: segmentation fault and bad global exclusion count Ambrish (Tue Oct 23 2007 - 01:45:05 CDT)
- equil_mode2.namd (2817 bytes)
- (no subject) ramya narasimhan (Tue Oct 23 2007 - 00:45:16 CDT)
- resmd.conf (1590 bytes)
- Molecule drifts and high average RMSD per residue Ambrish (Mon Oct 08 2007 - 11:02:49 CDT)
- npt_model1.namd (1635 bytes)
- question regarding nearest-image resolution in NAMD Vincent Kraeutler (Mon Sep 03 2007 - 03:23:24 CDT)
- signature.asc (250 bytes)
- Re: Recommended solvation box size Vincent Kraeutler (Wed Aug 29 2007 - 07:46:48 CDT)
- signature.asc (250 bytes)
- Re: Re: pressure vs density tip3p Vincent Kraeutler (Mon Aug 27 2007 - 16:55:47 CDT)
- signature.asc (250 bytes)
- Re: pressure vs density tip3p Roy Kimura (Mon Aug 27 2007 - 16:04:24 CDT)
- roy.kimura.vcf (262 bytes)
- pressure vs density tip3p Roy Kimura (Mon Aug 27 2007 - 15:54:40 CDT)
- roy.kimura.vcf (262 bytes)
- Re: setting solvent density during solvation jestin mandumpal (Mon Aug 27 2007 - 01:05:32 CDT)
- Re: How to implement an additional interaction potential? Vincent Kraeutler (Thu Aug 23 2007 - 07:53:05 CDT)
- signature.asc (250 bytes)
- How to implement an additional interaction potential? Philipp Schön (Thu Aug 23 2007 - 07:00:12 CDT)
- smime.p7s (1764 bytes)
- Re: energy drift in NVE Vincent Kraeutler (Mon Aug 20 2007 - 02:22:49 CDT)
- 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)
- signature.asc (250 bytes)
- Re: Re: NAMD: Exiting Prematurely Vincent Kraeutler (Wed Aug 15 2007 - 14:06:44 CDT)
- signature.asc (250 bytes)
- How to avoid => ERROR: Step 100920 cell rescaling factor limited. Philipp Schön (Mon Aug 13 2007 - 07:28:39 CDT)
- smime.p7s (1764 bytes)
- Re: Storage of large files Vincent Kraeutler (Thu Aug 09 2007 - 04:03:32 CDT)
- signature.asc (250 bytes)
- Re: Is very slow heating "bad"? Vincent Kraeutler (Sat Aug 04 2007 - 11:06:11 CDT)
- signature.asc (250 bytes)
- no effect on velocity scaling Philipp Schön (Fri Aug 03 2007 - 02:36:19 CDT)
- smime.p7s (1764 bytes)
- Re: Steered MD with NAMD? Vincent Kraeutler (Thu Aug 02 2007 - 14:47:06 CDT)
- 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)
- signature.asc (250 bytes)
- Re: Question regarding NAMD nonbonded routines Vincent Kraeutler (Fri Jul 27 2007 - 12:57:28 CDT)
- 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)
- signature.asc (250 bytes)
- Re: Question regarding NAMD nonbonded routines Vincent Kraeutler (Thu Jul 26 2007 - 12:27:29 CDT)
- signature.asc (250 bytes)
- Question regarding NAMD nonbonded routines Vincent Kraeutler (Wed Jul 25 2007 - 11:55:40 CDT)
- signature.asc (250 bytes)
- A serious problem of NAMD output. Wang, Boyang (Tue Jul 24 2007 - 17:35:08 CDT)
- rotlectr0.psf (424 bytes)
- Re: ATP molecule snoze pa (Thu Jul 19 2007 - 12:40:35 CDT)
- ATP.pdb (5022 bytes)
- Restarting calculation missmatches Alexandre A. Vakhrouchev (Thu Jul 19 2007 - 00:59:36 CDT)
- vz_avg.png (4590 bytes)
- Re: removing waters from big dcd files Dong Luo (Mon Jul 16 2007 - 23:00:25 CDT)
- DCDframe.zip (20082 bytes)
- balck box: what is the coupling constant when using langenvinFile? Philipp Schön (Fri Jul 13 2007 - 06:53:38 CDT)
- smime.p7s (1764 bytes)
- TCL: force not a vector Peter Jones (Tue Jul 10 2007 - 21:39:04 CDT)
- tcl_forces_E (3276 bytes)
- Problems with using multiple Tclforces scripts sequentially maria goranovic (Tue Jul 10 2007 - 12:46:48 CDT)
- cons196.tcl (1600 bytes)
- can i somehow use reassigntemp for selected atoms only? Philipp Schön (Tue Jul 10 2007 - 11:06:51 CDT)
- smime.p7s (1764 bytes)
- Did anybody really use TIP4P? Alessio Alexiadis (Mon Jul 09 2007 - 09:52:47 CDT)
- 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)
- LINUX_PWR5.tar.gz (2606 bytes)
- Re: ABF restrain alex digenova bravo (Thu Jul 05 2007 - 11:48:12 CDT)
- ABF.dat (5959 bytes)
- Re: Count protein solvent HBs? Dong Luo (Thu Jul 05 2007 - 09:21:36 CDT)
- hbonds.tcl (20260 bytes)
- problem with periodic boundaries Philipp Schön (Tue Jul 03 2007 - 10:13:04 CDT)
- smime.p7s (1764 bytes)
- Re: Changing loop to helix: restraining about 20 dihedral angles Jerome Henin (Sun Jun 24 2007 - 11:37:53 CDT)
- dummy.tcl (287 bytes)
- negative force shivam ghosh (Fri Jun 22 2007 - 00:42:24 CDT)
- 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)
- attachment.zip (1352 bytes)
- Re: Re: heat diffusion calculation QJos=E9_R=2E_Sabino=22?= (Mon Jun 18 2007 - 14:11:17 CDT)
- jrsabino.vcf (511 bytes)
- Re: Energy shift during simulation Cesar Luis Avila (Tue May 29 2007 - 09:53:31 CDT)
- energy.png (23524 bytes)
- basic pdb file run with namd and vmd Kayode Karunwi (Wed May 23 2007 - 16:05:01 CDT)
- alanine.pdb (1139 bytes)
- alanine.pgn.txt (168 bytes)
- alanine2.pdb (1092 bytes)
- alanine2.psf (3169 bytes)
- alanine2_wb.pdb (17412 bytes)
- alanine2_ws.pdb (1092 bytes)
- wat_sphere_alanine.tcl.txt (2089 bytes)
- Minimization Rita Cassia (Wed May 16 2007 - 12:19:51 CDT)
- 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)
- 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)
- hbond.tcl (2269 bytes)
- Re: files for air Jeffrey J. Potoff (Fri May 11 2007 - 07:21:20 CDT)
- Re: query about wrapped coordinates Gianluca Interlandi (Fri May 04 2007 - 14:54:20 CDT)
- DOC_unwrap.html (1140 bytes)
- unwrap.tcl (4957 bytes)
- abrupt deviation in rmsd values Monika Sharma (Wed May 02 2007 - 10:35:38 CDT)
- rmsd.dat (9927 bytes)
- Re: dcd binary file format Jeffrey A Tibbitt (Tue May 01 2007 - 16:57:47 CDT)
- syspart_dcd2 (6668 bytes)
- Re: Pressure Discrepancy Morad Alawneh (Fri Apr 20 2007 - 12:30:37 CDT)
- acf_pressure.pdf (2827 bytes)
- Re: Pressure Discrepancy Morad Alawneh (Fri Apr 20 2007 - 10:56:07 CDT)
- acf_pressure.pdf (22361 bytes)
- Re: Pressure Discrepancy Morad Alawneh (Tue Apr 03 2007 - 11:39:08 CDT)
- acf_pressure.pdf (17244 bytes)
- It doesn't work with using amber files. Hidekazu WATANABE (Thu Mar 29 2007 - 07:09:25 CDT)
- r800.new.pdb (3641 bytes)
- Help !!! ERROR: Atoms mooving too fast Juan Diaz (Tue Mar 27 2007 - 18:21:05 CDT)
- 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)
- top.inp.inp (929 bytes)
- Premature stop paco ty (Thu Mar 08 2007 - 03:57:15 CST)
- logfile.txt (7131 bytes)
- RDF.tcl question Jianhui Tian (Wed Feb 21 2007 - 12:43:24 CST)
- RDF.tcl (10381 bytes)
- Temperature problem Al-Rawi, Ahlam (Tue Feb 13 2007 - 14:05:35 CST)
- equ1.conf (1602 bytes)
- RE: DMPC psf. Lea Thřgersen (Fri Feb 09 2007 - 16:33:01 CST)
- DMPC.pdbalias (1281 bytes)
- "atoms moving too fast" error in bilayer simulation Himanshu Khandelia (Fri Feb 02 2007 - 07:31:53 CST)
- pope.in (1688 bytes)
- minimizing bad system: bad global excl. count Himanshu Khandelia (Tue Jan 23 2007 - 11:32:41 CST)
- config.in (1548 bytes)
- Stray PME grid charges detected Simon Watson (Tue Jan 09 2007 - 12:06:53 CST)
- 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)
- CHAPSO_H.pdb (8304 bytes)
- Is it equilibrated? taojinwuhan_at_sohu.com (Mon Dec 04 2006 - 01:45:49 CST)
- _____Microsoft_Word_____.doc (41472 bytes)
- error message in free energy pert. OMAR NABEEL ALY DEMERDASH (Sun Nov 26 2006 - 23:36:23 CST)
- 2eck_chrmv157_fep.conf (3179 bytes)
- LINE=*CMAP* regafan_at_usc.es (Wed Nov 22 2006 - 08:32:24 CST)
- min.log.gz (1221 bytes)
- ABF (fwd) Matthew Davies (Tue Nov 14 2006 - 07:40:30 CST)
- MHC_10_20.dat (2460 bytes)
- MHC_15_20.dat (1260 bytes)
- equilibration of protein Dhiraj Srivastava (Wed Nov 01 2006 - 12:31:17 CST)
- RMSD.doc (34816 bytes)
- Question about ABF Gaurav Sharma (Wed Oct 25 2006 - 18:03:13 CDT)
- ABF.doc (31744 bytes)
- Re: Warnings of psfgen Vishal Kopardé (Wed Oct 25 2006 - 17:09:15 CDT)
- pastedGraphic.pdf (25458 bytes)
- Warnings of psfgen Vishal Kopardé (Wed Oct 25 2006 - 08:37:30 CDT)
- out2 (18463 bytes)
- Re: phi and psi dihedral restraints luca (Mon Oct 23 2006 - 15:07:25 CDT)
- esempio_tcl_force.txt (2184 bytes)
- Multiple tclForcesScript Morad Alawneh (Sat Oct 14 2006 - 14:53:28 CDT)
- cylindrical_restraint.tcl (5593 bytes)
- spherical_restraint.tcl (5398 bytes)
- Re: "wrapAll on" with a complex Jerome Henin (Thu Oct 05 2006 - 22:08:18 CDT)
- DOC_unwrap.html (1140 bytes)
- unwrap.tcl (4957 bytes)
- Re: DPPC.Pdb file needed Elsa S. Henriques (Tue Sep 05 2006 - 08:42:29 CDT)
- DPPC.crd (9254 bytes)
- DPPC.Pdb file needed Lechuga, Javier (Mon Sep 04 2006 - 11:27:49 CDT)
- DPPC.pdb (9102 bytes)
- Re: CoordinateTransformation Sting (Sun Sep 03 2006 - 20:17:21 CDT)
- align_axis.tcl.txt (496 bytes)
- questions regarding output data of an ABF simulation Anahita Tafvizi (Mon Aug 07 2006 - 15:27:34 CDT)
- cons-dir.namd (12984 bytes)
- Re: RDF.tcl griadi_at_utalca.cl (Fri Jul 28 2006 - 17:01:24 CDT)
- counting_waters.tcl (1199 bytes)
- simulation crashing with nan Jackie (Wed Jul 26 2006 - 08:49:56 CDT)
- Problem.doc (25088 bytes)
- Re: psfgen gets ATP chiral atoms wrong Peter Freddolino (Tue Jul 25 2006 - 10:44:11 CDT)
- fixed.tgz (2937 bytes)
- Re: Queries on patches, GDP-topology Leonardo Trabuco (Mon Jul 24 2006 - 14:20:17 CDT)
- top_gdp.rtf (2707 bytes)
- Angle 2, Where is the problem [IMPORTANT] linefinc (Mon Jun 19 2006 - 11:50:41 CDT)
- 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)
- NPT.conf (3364 bytes)
- RE: Factorization in PMEGridSize JC Gumbart (Wed Jun 07 2006 - 09:25:24 CDT)
- image001.gif (339 bytes)
- the patch between segments for multiple chains molecule. Moumita Maiti (Fri Jun 02 2006 - 12:14:58 CDT)
- 1kx5.pgn (1369 bytes)
- Large energy fluctuation Sting (Mon May 30 2005 - 21:44:44 CDT)
- minimize.int (1261 bytes)
- Large energy fluctuation Sting (Fri Apr 08 2005 - 07:09:07 CDT)
- minimize.int (1261 bytes)
- questions regrading ABF Jan Saam (Mon May 29 2006 - 10:47:48 CDT)
- alanine.dat (1711 bytes)
- LDB problem on Dual Atlon64 X2 Sebastian Wasilewski (Wed May 17 2006 - 17:07:17 CDT)
- smime.p7s (3122 bytes)
- Re: namd: adding water molecules Mgr. Lubos Vrbka (Fri May 12 2006 - 00:51:02 CDT)
- smime.p7s (2341 bytes)
- periodic cell too small genie lfs (Wed May 10 2006 - 04:48:44 CDT)
- second.namd (2067 bytes)
- third.namd (2042 bytes)
- fourth.namd (2013 bytes)
- Re: why pressure is fluctuating so much Mgr. Lubos Vrbka (Fri Apr 28 2006 - 00:40:45 CDT)
- smime.p7s (2341 bytes)
- scaling NAMD2.6B1 on IBM P5 Thomas C. Bishop (Tue Apr 25 2006 - 14:44:33 CDT)
- dyn.NN.conf (2233 bytes)
- error related to tcl boundary forces gbellesia_at_chem.ucsb.edu (Tue Apr 25 2006 - 00:52:38 CDT)
- kffe.conf (2726 bytes)
- Re: NAMD-L: question about harmonic constraints JC Gumbart (Tue Apr 11 2006 - 17:41:08 CDT)
- cv_deca.tcl (2165 bytes)
- error about tclForcesScript xiaojing gong (Mon Apr 10 2006 - 09:21:13 CDT)
- min_2.log (3130 bytes)
- parameter file for DAD Yu Wang (Fri Apr 07 2006 - 09:18:55 CDT)
- wy0519.vcf (268 bytes)
- Simulation failed during the stage of heat Shulin Zhuang (Thu Mar 23 2006 - 23:58:15 CST)
- heating.namd (2255 bytes)
- Re: area per lipid for a protein embedded membrane system Nicolas Sapay (Sat Mar 11 2006 - 04:42:32 CST)
- area.tar.gz (6398 bytes)
- Re: Aligning structures Peter Freddolino (Thu Mar 09 2006 - 21:37:05 CST)
- align_frames.tcl (409 bytes)
- Re: Spherical harmonic restraint Morad Alawneh (Thu Mar 02 2006 - 13:25:39 CST)
- keep_water_out.tcl (7636 bytes)
- question on membrane crushing Longzhu Shen (Thu Mar 02 2006 - 15:18:09 CST)
- eqmd.in (2610 bytes)
- Re: Alchemical Free Energy Perturbation jsachs_at_mail.csb.yale.edu (Wed Mar 01 2006 - 15:31:07 CST)
- asa_dual.pdb (3076 bytes)
- asa_alchemify.psf (10667 bytes)
- fep.namd (1538 bytes)
- Alchemical Free Energy Perturbation Jawahar Neelankatan (Sat Feb 25 2006 - 00:40:02 CST)
- Alchemical Free Energy Perturbation Jawahar Neelankatan (Sat Feb 25 2006 - 01:36:29 CST)
- Free Cluster-Building Workshops - 16-17 Mar 2006, 20-21 Apr 2006 Tim Skirvin (Mon Feb 13 2006 - 14:41:24 CST)
- part (186 bytes)
- Fwd: Water Box size snoze pa (Fri Feb 10 2006 - 10:58:27 CST)
- namdmin.png (90535 bytes)
- namd1ns.png (97173 bytes)
- pairInteractionSelf Yu Wang (Fri Feb 10 2006 - 03:19:34 CST)
- 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)
- splitmultiframepdb2files.tcl (781 bytes)
- Re: velocity error, still bo baker (Wed Jan 11 2006 - 16:20:37 CST)
- NPT2-011006.conf (1213 bytes)
- NPT3-011006.conf (1233 bytes)
- velocity error, still bo baker (Tue Jan 10 2006 - 15:20:58 CST)
- NPT1-011006.conf (1213 bytes)
- same random numbers?? Shahid Qamar (Fri Jan 06 2006 - 15:49:01 CST)
- random.txt (959 bytes)
- Re: velocity error bo baker (Thu Jan 05 2006 - 18:02:35 CST)
- Re: Energy Plugin bo baker (Wed Jan 04 2006 - 16:26:24 CST)
- velocity error bo baker (Wed Jan 04 2006 - 13:12:45 CST)
- FATAL ERROR: unknown floating-point error, errno = 4 Manori Indira Jayasinghe (Thu Dec 22 2005 - 23:16:41 CST)
- 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)
- 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)
- popc_s.conf (1703 bytes)
- Re: ABF Simulation Jérôme Hénin (Fri Oct 28 2005 - 04:05:52 CDT)
- vectors.tcl (10343 bytes)
- scaling issue Robert Bjornson (Fri Oct 21 2005 - 15:56:13 CDT)
- prod2.namd (2773 bytes)
- apoa1.namd (851 bytes)
- Re: namdplot: command not found Robert Brunner (Thu Oct 13 2005 - 15:11:37 CDT)
- Re: namdplot: command not found bo baker (Tue Oct 11 2005 - 18:56:10 CDT)
- namdplot (3535 bytes)
- Re: namdplot: command not found Robert Brunner (Tue Oct 11 2005 - 10:32:00 CDT)
- RE: autoionize & namd2 Michel Espinoza-Fonseca (Thu Sep 22 2005 - 02:51:08 CDT)
- test.in (1882 bytes)
- problem when heating the system Phoenix (Mon Aug 29 2005 - 23:07:42 CDT)
- heat.cfg (1198 bytes)
- ERROR: Margin is too small (BUG?) Mauricio Carrillo Tripp (Wed Aug 03 2005 - 10:02:42 CDT)
- 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)
- dcdcellfix.tar (102400 bytes)
- Velocity after heating mustapha.hamdi_at_ensi-bourges.fr (Mon Jul 18 2005 - 06:56:03 CDT)
- position_restrained.log (13533 bytes)
- Re: Runnig same config file many times Mauricio Carrillo Tripp (Fri Jul 15 2005 - 17:33:48 CDT)
- namd.csh (513 bytes)
- RE: Adding Misc. Potentials (e.g. spherical/repulsive restraints/constraints ) JC Gumbart (Wed Jun 29 2005 - 11:18:23 CDT)
- keep_water_out.tcl (7635 bytes)
- Re: catdcd and dcdunitcell Jérôme Hénin (Tue Jun 28 2005 - 09:14:32 CDT)
- catdcd.gz (12558 bytes)
- autoimd on windows Anna Modzelewska (Mon Jun 20 2005 - 06:40:29 CDT)
- autoimd.log (2741 bytes)
- How to conservate energy during NVE simulations??? Leonardo Sepulveda Durán (Wed Jun 15 2005 - 20:55:29 CDT)
- equil_data1_TempPresTotEn.pdf (48858 bytes)
- Re: Multiple Harmonic Constraints Sascha Tayefeh (Thu Jun 09 2005 - 08:28:52 CDT)
- sascha.vcf (372 bytes)
- Multiple Harmonic Constraints Sascha Tayefeh (Thu Jun 09 2005 - 02:31:38 CDT)
- sascha.vcf (372 bytes)
- config files Mark A. Hallman (Tue Jun 07 2005 - 12:17:35 CDT)
- minimize.namd (882 bytes)
- Re: NADP problem Hemant Kushwaha (Fri Jun 03 2005 - 22:07:08 CDT)
- nadp.top (11769 bytes)
- Re: NADP problem Hemant Kushwaha (Fri Jun 03 2005 - 08:28:56 CDT)
- nadp.top (11768 bytes)
- about *.psf ËďćĂćĂ (Thu May 26 2005 - 23:59:07 CDT)
- lig1.gif (3592 bytes)
- Re: Re: Simulated Annealing Config Leonardo Sepulveda Durán (Tue May 24 2005 - 14:55:49 CDT)
- ubq.conf (3346 bytes)
- What's wrong with my namd2 Xiaoqing Wang (Sun May 15 2005 - 07:01:13 CDT)
- 8 (959438 bytes)
- Re: Leandro Martínez (Fri Apr 08 2005 - 13:50:34 CDT)
- atomnames.f (3102 bytes)
- Re: NMAD job abnormally killed with PBS Chris Samuel (Wed Apr 06 2005 - 22:32:01 CDT)
- part (190 bytes)
- Re: FATAL ERROR: Stale NFS file handle Chris Samuel (Wed Apr 06 2005 - 22:29:59 CDT)
- part (190 bytes)
- RATTLE and DNA Nicholas M Glykos (Tue Apr 05 2005 - 05:33:48 CDT)
- Re: problem running namd Chris Samuel (Mon Apr 04 2005 - 18:10:58 CDT)
- part (190 bytes)
- Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Chris Samuel (Wed Mar 30 2005 - 00:05:44 CST)
- part (190 bytes)
- Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Chris Samuel (Sun Mar 20 2005 - 20:04:50 CST)
- part (190 bytes)
- Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Chris Samuel (Thu Mar 17 2005 - 23:23:24 CST)
- part (190 bytes)
- Re: Compiling on Linux-PPC970-Myrinet-MPI-xlC Chris Samuel (Wed Mar 16 2005 - 00:06:21 CST)
- part (190 bytes)
- Re: G5 clusters Gengbin Zheng (Tue Mar 08 2005 - 12:44:25 CST)
- apoa1_bench.png (12517 bytes)
- Re: segmentation violation!! Robert Brunner (Tue Jan 18 2005 - 11:05:00 CST)
- PGP.sig (187 bytes)
- multiple jobs on a cluster Cheri M Turman (Wed Jan 12 2005 - 15:55:42 CST)
- cturman.vcf (336 bytes)
- about MCTI output mashaojie163 (Mon Dec 27 2004 - 01:29:36 CST)
- clip_image002.gif (168 bytes)
- clip_image002.gif (315 bytes)
- clip_image002.gif (168 bytes)
- clip_image002.gif (147 bytes)
- FATAL ERROR: Asymmetric water molecule ? Gaurav Sharma (Tue Dec 21 2004 - 14:58:11 CST)
- 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)
- md_script (841 bytes)
- fep_script (665 bytes)
- Re: Variation of results in iterations Robert Brunner (Mon Dec 06 2004 - 21:15:00 CST)
- PGP.sig (187 bytes)
- Re: NAMD on Xeon EM64T Chris Samuel (Thu Dec 02 2004 - 22:18:39 CST)
- part (190 bytes)
- Re: NAMD Source Robert Brunner (Fri Nov 19 2004 - 10:54:16 CST)
- PGP.sig (187 bytes)
- Rif: Re: Rif: Re: Rif: Re: Rif: Re: linux cluster trouble max (Fri Nov 19 2004 - 03:47:01 CST)
- linux cluster trouble max (Tue Nov 16 2004 - 04:44:36 CST)
- IMSTP.gif (494 bytes)
- Rif: Re: linux cluster trouble max (Wed Nov 10 2004 - 03:00:42 CST)
- IMSTP.gif (494 bytes)
- Re: Sample Configuratiion files Cheri M Turman (Wed Nov 03 2004 - 19:47:25 CST)
- cturman.vcf (336 bytes)
- Re: System minimization: fail after 199 steps Charles Danko (Wed Nov 03 2004 - 11:53:06 CST)
- minimize.namd (2698 bytes)
- Tcl dihedral restraints in CG minimisation Ben Roberts (Tue Nov 02 2004 - 17:01:28 CST)
- restraints.tcl (13840 bytes)
- Re: [Periodic Boundary]: from charmm to namd Sascha Tayefeh (Tue Nov 02 2004 - 12:46:02 CST)
- sascha.vcf (397 bytes)
- [Periodic Boundary]: from charmm to namd Sascha Tayefeh (Tue Nov 02 2004 - 09:08:42 CST)
- sascha.vcf (397 bytes)
- HEM residue in NAMD Peter Bazeley (Tue Nov 02 2004 - 02:23:50 CST)
- 2D6H_fixed_heme_bak.pdb (6068 bytes)
- FK506 ligand topology file(1FKF) MERIC AYSE OVACIK (Thu Oct 28 2004 - 05:29:21 CDT)
- 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)
- part (190 bytes)
- Re: NAMD on Linux cluster with Myrinet Chris Samuel (Mon Oct 18 2004 - 23:02:27 CDT)
- part (190 bytes)
- bug report and stray pme Cheri M Turman (Mon Oct 18 2004 - 16:23:42 CDT)
- cturman.vcf (336 bytes)
- [Fwd: counterion software] Cetin Baloglu (Sun Oct 10 2004 - 23:55:20 CDT)
- cetinb.vcf (342 bytes)
- counterion software Cetin Baloglu (Sun Oct 10 2004 - 23:51:56 CDT)
- cetinb.vcf (342 bytes)
- Fw: Constraint failure in RATTLE algorithm Zhong Wenyu (Sun Sep 19 2004 - 02:14:27 CDT)
- open4.namd (2190 bytes)
- open4.log (19290 bytes)
- Re: Compilation on Opteron Chris Samuel (Thu Aug 26 2004 - 00:04:07 CDT)
- part (190 bytes)
- RE: radial distribution function Liu, Zhanwu (Fri Aug 13 2004 - 08:40:51 CDT)
- 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)
- Add_Atoms_to_PDBs.pl (3307 bytes)
- HYP files Ivan Vinogradov (Tue Aug 03 2004 - 12:55:52 CDT)
- top_hyp.inp (2006 bytes)
- par_hyp.inp (351 bytes)
- charm++ MPICH and Myrinet Mauricio Carrillo Tripp (Mon Jul 26 2004 - 17:34:53 CDT)
- 01.log (11715 bytes)
- Warning: Not all atoms have unique coordinates. Shirley Hui (Thu Jul 08 2004 - 09:25:13 CDT)
- cpc.conf (2926 bytes)
- Re: icc compilation problem Chris Samuel (Sun Jul 04 2004 - 20:41:14 CDT)
- part (190 bytes)
- Re: icc compilation problem Chris Samuel (Thu Jul 01 2004 - 18:11:57 CDT)
- part (190 bytes)
- pmf error mashaojie163 (Mon Jun 21 2004 - 10:17:20 CDT)
- Simulated Annealing Config Ahmet Bakan (Tue Jun 15 2004 - 08:24:59 CDT)
- Re: Force Calculation in NAMD Gadi Oron (Sun May 23 2004 - 02:37:27 CDT)
- 8859-8 (2126 bytes)
- Why Vmd didn't show the Pt-Cl bond myang (Wed May 19 2004 - 18:46:31 CDT)
- K2PtCl6_less.pdb (1865 bytes)
- autoionize script amodzelewska_at_dns.iimcb.gov.pl (Sun May 16 2004 - 13:21:58 CDT)
- ions.top (1176 bytes)
- installing on beowulf cluster Cheri M Turman (Sun May 09 2004 - 19:58:25 CDT)
- cturman.vcf (336 bytes)
- installing on beowulf cluster Cheri M Turman (Thu May 06 2004 - 13:38:16 CDT)
- 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)
- cnt_mod3.out (5817 bytes)
- cnt_mod3.conf (2999 bytes)
- RE: Binding free energy of a protein complex Ahmet Bakan (Mon May 03 2004 - 06:02:29 CDT)
- hbond.tcl (3461 bytes)
- problems with namdplot fixed by using new plotting program Cheri M Turman (Tue Apr 27 2004 - 16:34:42 CDT)
- cturman.vcf (336 bytes)
- temperature question in logfile Cheri M Turman (Tue Apr 20 2004 - 17:13:28 CDT)
- cturman.vcf (336 bytes)
- Re: still problems with namdplot Gadi Oron (Sun Apr 18 2004 - 01:51:42 CDT)
- still problems with namdplot Cheri M Turman (Thu Apr 15 2004 - 14:13:57 CDT)
- cturman.vcf (336 bytes)
- Re: More NAMD/gm2 problems Chris Samuel (Wed Mar 31 2004 - 00:40:36 CST)
- charmc.patch (349 bytes)
- mpicc.h (200 bytes)
- mpicc.sh (538 bytes)
- A tool to set up alchemical FEP transformations Jérôme Hénin (Mon Mar 29 2004 - 10:27:12 CST)
- alchemify.tar.gz (20572 bytes)
- Re: CP3-NH3 error Tim Isgro (Thu Mar 04 2004 - 13:56:44 CST)
- HERGpsfgen.txt (508 bytes)
- Re: Minimization with CHARMM Tim Isgro (Mon Feb 09 2004 - 17:04:13 CST)
- sample.conf (4331 bytes)
- RE: minimization problem - "Bad global exclusion count,possible error!" Frances Leung (Fri Jan 30 2004 - 02:52:09 CST)
- psfgen_log.txt (52161 bytes)
- minimization problem - "Bad global exclusion count, possible error!" Frances Leung (Thu Jan 29 2004 - 19:25:27 CST)
- minimize_log.txt (15543 bytes)
- Parameters and topologies for aa at different protonation states Bartosz Dobrzelecki (Fri Jan 23 2004 - 06:45:26 CST)
- signature.asc (190 bytes)
- missing atoms warnings for psfgen Frances Leung (Mon Jan 19 2004 - 21:47:33 CST)
- psflog.txt (142065 bytes)
- Potential Terms AHMET BAKAN (Mon Jan 05 2004 - 12:20:02 CST)
- 2_Theory.fm.anc.gif (13045 bytes)
- alchemical free energy perturbation AMIT PALIWAL (Mon Jan 05 2004 - 00:37:05 CST)
- growth.namd (1866 bytes)
- system.fep (450 bytes)
- Simulating RNA+PROTEIN complexes Bartosz Dobrzelecki (Fri Dec 19 2003 - 14:30:23 CST)
- signature.asc (190 bytes)
- Re: Help! unstable simulation - ARG go nuts... Gadi Oron (Tue Dec 16 2003 - 09:33:25 CST)
- snap.png (53801 bytes)
- Re: Help! unstable simulation. Alexandre Vakhrouchev (Fri Dec 12 2003 - 03:16:55 CST)
- psf.log (5144 bytes)
- simulated annealing script Cheri M Turman (Thu Sep 25 2003 - 13:15:10 CDT)
- cturman.vcf (336 bytes)
- Re: Re: seg fault and namdplot problem Cheri M Turman (Mon Sep 22 2003 - 18:58:30 CDT)
- cturman.vcf (336 bytes)
- Re: seg fault and namdplot problem Cheri M Turman (Mon Sep 22 2003 - 16:22:46 CDT)
- cturman.vcf (336 bytes)
- segmentation fault Cheri M Turman (Tue Sep 16 2003 - 14:12:43 CDT)
- W1A1_wb.log (15255 bytes)
- cturman.vcf (336 bytes)
Last message date: Sat Nov 07 2009 - 03:09:56 CST
Archived on: Sat Nov 07 2009 - 12:19:01 CST
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