Re: [gmx-users] compatibility of MOPAC charges with GROMACS ?
On Wed, May 16, 2007 at 05:16:49PM -0700, David Mobley wrote: So what you really need to do, once you have worked out which forcfield you are going to use, go back to the documentation / papers for that particular forcefield, see how they generated the parameters, then use that same procedure for the new parameters / molecules you want to generated. Strangely enough, I recall writing almost exactly the same thing in response to a different user yesterday or the day before. It will sure be nice when the Wiki is working, then we only have to answer this once. ..and RTFW will replace RTFM.. marc ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] error in topology file generation
*hello everybody,* *i am new user to GROMACS,* *i want to perform simulations on docked protein ligand complex,* *During the conversion of the PDB file i came to such a problem: **just before the end of conversion the program pdb2gmx.exe told that my **PDB file compound is not included into Gromacs residue topology database. **Directly as it says: ** Fatal error: Residue ''M_3' not found in residue topology database *(which is docked ligand in the protein) *Woud you be so glad to tell me how can I resolve this problem? * looking forward to your help tahnks in advance. -- Archana Chavan MS (Pharm)Pharmacoinformatics National Institute of Pharmaceutical Education and Research (NIPER) Mohali-160 062 Punjab, India. phone:+91-(0)-947223 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Re: Error while doing EM in DMSO.
Dear David, Thanks for advice, i had made the changes but still getting the same error that Fatal error: Atomtype 'SD' not found! SDMSO 32.06000 ; DMSO Sulphur (solvent) CDMSO 15.03500 ; DMSO Carbon (solvent) ODMSO 15.99940 ; DMSO Oxygen (solvent) **Changes Made in ffG43a1.atp file*** SD 32.06000 ; DMSO Sulphur (solvent) CD 15.03500 ; DMSO Carbon (solvent) OD 15.99940 ; DMSO Oxygen (solvent) I am totally helpless and clueless in finding my mistakes.Any help,hint, suggestions are most welcome. Thanks, With Regards anil Today's Topics: 1. Re: Error while doing EM in DMSO. (David van der Spoel) Date: Wed, 16 May 2007 21:07:54 +0200 From: David van der Spoel [EMAIL PROTECTED] Subject: Re: [gmx-users] Error while doing EM in DMSO. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anil Kumar wrote: Dear Users, First of all thank you Mark, yes you are right. it was problem of force field and topoloy file mismatch. I have made changes in the ffG43a1 residue toplogy file for DMSO., but still getting the same error. Please let me know if i am doing some mistake. If the problem is the missing masses, then just add them in the [atoms] section. (Chapter 5) -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596,75124 Uppsala, Sweden phone:46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se +++ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Compiling Gromacs on 64 bit windows platform...
Hi guys, I am trying to compiler GROMACS onto 64 bit windows platform with AMD Opteron Machine with Windows 2003 Server R2. It may sound pretty basic but i am not able to figure out... I could see assembly code in nonbonded directory and i am trying to write makefile to build the same but i am bit confused as which directories/files should i compile and is it appropriate that i am using nasm to execute those assembly files on windows 64 bit platform? Any help/pointers would be highly appriciated. With warm regards, *KEDAR* ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] error in topology file generation
Archana Chavan wrote: /hello everybody,/ /i am new user to GROMACS,/ /i want to perform simulations on docked protein ligand complex,/ /During the conversion of the PDB file i came to such a problem: //just before the end of conversion the program pdb2gmx.exe told that my //PDB file compound is not included into Gromacs residue topology database. //Directly as it says: // Fatal error: Residue ''M_3' not found in residue topology database / (which is docked ligand in the protein) /Woud you be so glad to tell me how can I resolve this problem? / chapter 5 in the manual. looking forward to your help tahnks in advance. -- Archana Chavan MS (Pharm)Pharmacoinformatics National Institute of Pharmaceutical Education and Research (NIPER) Mohali-160 062 Punjab, India. phone:+91-(0)-947223 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Re: Error while doing EM in DMSO.
Anil Kumar wrote: Dear David, Thanks for advice, i had made the changes but still getting the same error that Fatal error: Atomtype 'SD' not found! SDMSO 32.06000 ; DMSO Sulphur (solvent) CDMSO 15.03500 ; DMSO Carbon (solvent) ODMSO 15.99940 ; DMSO Oxygen (solvent) **Changes Made in ffG43a1.atp file*** SD 32.06000 ; DMSO Sulphur (solvent) CD 15.03500 ; DMSO Carbon (solvent) OD 15.99940 ; DMSO Oxygen (solvent) I am totally helpless and clueless in finding my mistakes.Any help,hint, suggestions are most welcome. Thanks, With Regards anil Today's Topics: 1. Re: Error while doing EM in DMSO. (David van der Spoel) Date: Wed, 16 May 2007 21:07:54 +0200 From: David van der Spoel [EMAIL PROTECTED] Subject: Re: [gmx-users] Error while doing EM in DMSO. To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; charset=ISO-8859-1; format=flowed Anil Kumar wrote: Dear Users, First of all thank you Mark, yes you are right. it was problem of force field and topoloy file mismatch. I have made changes in the ffG43a1 residue toplogy file for DMSO., but still getting the same error. Please let me know if i am doing some mistake. If the problem is the missing masses, then just add them in the [atoms] section. (Chapter 5) -- they should be added in the top file. the atp is not used for anything (except for confusing people unfortunately) -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] FEP with real or dummy charges?
Hi I want to calculate the change in free energy (electrostatic contribution only) when introducing a charge in a certain site of a protein using a single step FEP. Should this be done with charging an inserted virtual site (a dummy atom) or a protein atom (e.g. Ca)? I noticed that in the case of the dummy atom, the Coul-14:Protein-vsite zero. I am not sure why though... Thanks a lot in advance for any feedback. Best wishes George Dr. George Patargias Polymer IRC Group University of Leeds Leeds, LS2 9JT, UK ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] how to increase the number of
Dear All, I am using GROMACS 3.3.1 and i setup a simulation to run in 2 nodes of a workstation. It is running OK however now i have two extra nodes available to use in the same box and i would like to speed up the sim by using them. Is there any way to increase the number of nodes under use ? I tried tpbconv to extend the sim and increase the np vaue but it did not worked. Thanks Afonso __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] question about g_rmsdist II
Sorry, since I hadn't any answer to my question yet, I'm resending it to give it visibility! Thanks, Fabrizio --- Messaggio inoltrato --- Da: Fabrizio Mancinelli [EMAIL PROTECTED] A: gmx-users@gromacs.org Oggetto: question about g_rmsdist Data: Mon, 14 May 2007 18:52:54 +0200 Dear all, I would like to have some elucidation about g_rmsdist output. Optionally, it outputs three matrices with the options -rms, -mean and - scl. Questions are: 1) Exploring .xpm files, I see there is a letter code which converts color exa-codes to letters to values. The resolution is tunable with option -nlevels, but the range is delimited by the highest calculated value. Is there a way to assign a fixed range (in order, e.g., to compare different trajectories of the same protein)? 2) -rms output, I guess, is the deviation from average distance, over time, for each atom couple. I see my matrix is full of 0's. I expected 0's on the principal diagonal (distance of an atom from itself is obviously always zero), but others? It should mean atoms' distances RMSD are 0, that is they do not deviate... but they don't look that fixed at all from the trajectory! This is even more surprisingly in the -mean output, which should contain, I guess, atom distances averaged over time. In that case there are lots of 0's too. Maybe my I guess are wrong... 3) What is, actually, -scl output? Thanks in advance to anybody who will answer. Fabrizio ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to increase the number of
Afonso Duarte wrote: Dear All, I am using GROMACS 3.3.1 and i setup a simulation to run in 2 nodes of a workstation. It is running OK however now i have two extra nodes available to use in the same box and i would like to speed up the sim by using them. Is there any way to increase the number of nodes under use ? I tried tpbconv to extend the sim and increase the np vaue but it did not worked. The other way to do a restart is to get your original .mdp file (check the values of gen_seed and unconstrained_start are appropriate), and your current .trr, .edr and any appropriate .gro (it's just used for atom names) and feed them to grompp with whatever -n flag you want to use. I expect this will not be reproducible with a tpbconv restart (particularly with PME) but you'll still be sampling the same ensemble within the error of the MD approximation. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] question about g_rmsdist II
Fabrizio Mancinelli wrote: Sorry, since I hadn't any answer to my question yet, I'm resending it to give it visibility! If you don't get any luck, remember that the source code is available for a reason :-) --- Messaggio inoltrato --- Da: Fabrizio Mancinelli [EMAIL PROTECTED] A: gmx-users@gromacs.org Oggetto: question about g_rmsdist Data: Mon, 14 May 2007 18:52:54 +0200 Dear all, I would like to have some elucidation about g_rmsdist output. Optionally, it outputs three matrices with the options -rms, -mean and - scl. Questions are: 1) Exploring .xpm files, I see there is a letter code which converts color exa-codes to letters to values. The resolution is tunable with option -nlevels, but the range is delimited by the highest calculated value. Is there a way to assign a fixed range (in order, e.g., to compare different trajectories of the same protein)? There was discussion on the list of implementing a way to write a binary or ascii matrix. This would make it easy to do the kind of comparison I think you want to do. Check the archives for the resolution, but if there was one suitable for your needs, you'd need to use the CVS version of this utility. 2) -rms output, I guess, is the deviation from average distance, over time, for each atom couple. I see my matrix is full of 0's. I expected 0's on the principal diagonal (distance of an atom from itself is obviously always zero), but others? It should mean atoms' distances RMSD are 0, that is they do not deviate... but they don't look that fixed at all from the trajectory! This is even more surprisingly in the -mean output, which should contain, I guess, atom distances averaged over time. In that case there are lots of 0's too. Maybe my I guess are wrong... You've certainly got the wrong handle on -mean. Check the man page. 3) What is, actually, -scl output? Don't know. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Compiling Gromacs on 64 bit windows platform...
Kedar Potdar wrote: Hi guys, I am trying to compiler GROMACS onto 64 bit windows platform with AMD Opteron Machine with Windows 2003 Server R2. It may sound pretty basic but i am not able to figure out... I could see assembly code in nonbonded directory and i am trying to write makefile to build the same but i am bit confused as which directories/files should i compile and is it appropriate that i am using nasm to execute those assembly files on windows 64 bit platform? Any help/pointers would be highly appriciated. I'm confused - why isn't normal configure and make (such as on the gromacs webpage installation instructions) working for you? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Compiling Gromacs on 64 bit windows platform...
I think, i forgot to mention that i am trying to compile GROMACS on native windows and not on Cygwin... On 5/17/07, Mark Abraham [EMAIL PROTECTED] wrote: Kedar Potdar wrote: Hi guys, I am trying to compiler GROMACS onto 64 bit windows platform with AMD Opteron Machine with Windows 2003 Server R2. It may sound pretty basic but i am not able to figure out... I could see assembly code in nonbonded directory and i am trying to write makefile to build the same but i am bit confused as which directories/files should i compile and is it appropriate that i am using nasm to execute those assembly files on windows 64 bit platform? Any help/pointers would be highly appriciated. I'm confused - why isn't normal configure and make (such as on the gromacs webpage installation instructions) working for you? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] same simulation, different results
Shutting off the fft optimization produced the same results for 3.2.1. Then I tried running two simulations using version 3.3.1 with the optimized fft and they differed. Your response seemed to imply that the newer version should produce identical results. Could you clear this up for me? Thank you, Jim Fonseca On May 16, 2007, at 9:40 AM, Jim Fonseca wrote: Thanks a lot--that was it. On May 15, 2007, at 12:42 PM, David van der Spoel wrote: Jim Fonseca wrote: Hi, Does anyone know what would cause a simulation to change if I run it a second time? I'm starting with an EM structure and just doing a quick 10 ps simulation. I've found that (in one case) the energies start to differ somewhere between step 200 and step 250--the Vir and Pres values differ first. I can't figure out what else besides gen_vel and gen_seed would give me different results. I'm running on the same system, same number of processors, etc. I'm pasting my .mdp below. I realize I'm probably overlooking something, but can anyone help me with this? Thank you, Jim Fonseca title= PG_Ca_ext cpp = /usr/bin/cpp include = -I../top constraints = all-bonds integrator = md tinit= 0.0 dt = 0.002 nsteps = 1 ;20 ps nstxout = 1 nstvout = 1 nstlog = 1 nstenergy= 50 nstxtcout= 50 xtc_grps = Protein SOL_Na_Ca POP energygrps = Protein SOL_Na_Ca POP nstlist = 10 ns_type = grid rlist= 1.4 coulombtype = PME rcoulomb = 1.4 rvdw = 1.4 tcoupl = Berendsen tc-grps = Protein SOL_Na_CaPOP tau_t= 0.1 0.1 0.1 ref_t= 300 300 300 Pcoupl = Berendsen pcoupltype = anisotropic tau_p= 1.0 compressibility = 4.5e-5 4.5e-5 4.5e-5 0.0 0.0 0.0 ref_p= 1.5 1.5 1.5 0.0 0.0 0.0 gen_vel = yes gen_temp = 300 gen_seed = 161803 optimize_fft = yes Is this 3.2.1? The optimize_fft may make your simulations differ because, depending on timing, a different algorithm may be used. Change this flag to no and test again. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David. _ ___ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se +++ + ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use thewww interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] same simulation, different results
Jim Fonseca wrote: Shutting off the fft optimization produced the same results for 3.2.1. Then I tried running two simulations using version 3.3.1 with the optimized fft and they differed. Your response seemed to imply that the newer version should produce identical results. Could you clear this up for me? Turning on the fftw optimization may lead to different results in either version. Turning it off should give identical results. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] question about g_rmsdist II
17 maj 2007 kl. 15.49 skrev Mark Abraham: Fabrizio Mancinelli wrote: Sorry, since I hadn't any answer to my question yet, I'm resending it to give it visibility! If you don't get any luck, remember that the source code is available for a reason :-) --- Messaggio inoltrato --- Da: Fabrizio Mancinelli [EMAIL PROTECTED] A: gmx-users@gromacs.org Oggetto: question about g_rmsdist Data: Mon, 14 May 2007 18:52:54 +0200 Dear all, I would like to have some elucidation about g_rmsdist output. Optionally, it outputs three matrices with the options -rms, -mean and - scl. Questions are: 1) Exploring .xpm files, I see there is a letter code which converts color exa-codes to letters to values. The resolution is tunable with option -nlevels, but the range is delimited by the highest calculated value. Is there a way to assign a fixed range (in order, e.g., to compare different trajectories of the same protein)? There was discussion on the list of implementing a way to write a binary or ascii matrix. This would make it easy to do the kind of comparison I think you want to do. Check the archives for the resolution, but if there was one suitable for your needs, you'd need to use the CVS version of this utility. 2) -rms output, I guess, is the deviation from average distance, over time, for each atom couple. I see my matrix is full of 0's. I expected 0's on the principal diagonal (distance of an atom from itself is obviously always zero), but others? It should mean atoms' distances RMSD are 0, that is they do not deviate... but they don't look that fixed at all from the trajectory! This is even more surprisingly in the -mean output, which should contain, I guess, atom distances averaged over time. In that case there are lots of 0's too. Maybe my I guess are wrong... You've certainly got the wrong handle on -mean. Check the man page. 3) What is, actually, -scl output? I don't use g_rmsdist much, but the -h option tells me that g_rmsdist can also produce matrices of the rms distances, rms distances scaled with the mean distance and the mean distances and matrices with NMR averaged distances (1/r^3 and 1/r^6 averaging)., which is a good clue. /Erik Don't know. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] bondtype 5
This may be a really simple question, I know, but still... How can I set up a fixed connection between two atoms of a molecule? When I choose the 5th bondtype in my topology-file I get the following output from grompp (though it's processing, so I CAN start mdrun afterwards): WARNING 1 [file ethane.itp, line 12]: No default Connect Bonds types, using zeroes Either way I'm not sure how the distance of these two atoms is processed, so there is NO parameter that is specifying this bond-type (and a constraint would be processed by gromacs, wouldn't it? And I don't want it to, cause I want the simulation to be as simple as possible) By the way, I wanna simulate a huge system of ethane and take a look at the processing time per simulated step, is there an output-file thats reading this? Thanks in advance to everyone who is replying, it's so hard when you're stuck. -- GMX FreeMail: 1 GB Postfach, 5 E-Mail-Adressen, 10 Free SMS. Alle Infos und kostenlose Anmeldung: http://www.gmx.net/de/go/freemail ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] bondtype 5
Nicolas Schmidt wrote: This may be a really simple question, I know, but still... How can I set up a fixed connection between two atoms of a molecule? When I choose the 5th bondtype in my topology-file I get the following output from grompp (though it's processing, so I CAN start mdrun afterwards): WARNING 1 [file ethane.itp, line 12]: No default Connect Bonds types, using zeroes Either way I'm not sure how the distance of these two atoms is processed, so there is NO parameter that is specifying this bond-type (and a constraint would be processed by gromacs, wouldn't it? And I don't want it to, cause I want the simulation to be as simple as possible) By the way, I wanna simulate a huge system of ethane and take a look at the processing time per simulated step, is there an output-file thats reading this? Thanks in advance to everyone who is replying, it's so hard when you're stuck. [ constraint ] ; i j type length 1 2 1 0.15 -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with genion
Hi gromacs-users, I have a problem with the simulation of a capped lysine residue.I followed the tutorial step by step. I added 1 Cl ion into my system in order to neutralize the overall charge by using genion, and then used the grompp command and I encountered with the following error: Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 891 Fatal error: moleculetype CU1+ is redefined What is the problem? Thanks in advance Ozge Engin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] initial configuration problems and energy minimization
Dear gmx-users, Here I have a some problem regarding initial configuration My system is composed of cationic surfactants, co-surfactants, water. I am able to minimize the energy of my system(random), if it contains 15(surfactants)+ 15(co-surf)+ 1000(water)+ 15 (counterions) and also am able to simulate... But when I increase the number of surfactants or co-surfactants. Even the energy of the system initially is a big negative. When I start true simulation, Potential energy is becoming positive...and ultimately box is exploding [xtc error or some times ci error].. still I tried to minimize the energy of initial configuration, but I am getting the same error. Below I describe the steps i took to do simulations 1)minimize the energy of surfactnat(btm.gro)(includes counterion) and co-surfactant(str.gro) in Vaccum 2)Generate a system of 100 surfactnats(includes counterions), 20 co-surfactants and 1000 waters by using packmol(random) 3)Minimize the whole system until potential will become a reasonable negaive 4)With that minimized structure I run simulation but always the box is exploding My simulation is successful when the no of surf and co-surf are 15+15 For this successful simulation Initially i am conducting a NVT simulation with 0.01 fs timestep at 100K temp and then another NVT at desired temp(300K) and then NPT with 2fs timestep I don't know why I am unable to conduct with more no. of surfactants in water. I tried the samething for a bilayer initial configuration also(generated by packmol), but getting same error Is there any solution to solve this??? I already checked archive lot of times but i am unable to find anything relevant. I think its not that much related to gromacs.. But i need help to solve this problem I can give any more details if it is needed. Thanks in advance -- Arun kumar.V M.E Chemical, IISc ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Calculate individual force between each atom pair
Hi, Everyone, The force given by .trr file is the total force acted on each atom. Now I would like to modify codes to calculate individaul force between each atom pair. Is it possible in gromacs? (Because I remember some part of gromacs is writen in Fortran and already compiled). Thanks in advance. Yours Sincerely, WU Yanbin ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] bondtype 5
By the way, I wanna simulate a huge system of ethane and take a look at the processing time per simulated step, is there an output-file thats reading this? Have you tried looking at the bottom of your normal output? Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with genion
OZGE ENGIN wrote: Hi gromacs-users, I have a problem with the simulation of a capped lysine residue.I followed the tutorial step by step. I added 1 Cl ion into my system in order to neutralize the overall charge by using genion, and then used the grompp command and I encountered with the following error: Program grompp, VERSION 3.3.1 Source code file: toppush.c, line: 891 Fatal error: moleculetype CU1+ is redefined What is the problem? The molecule named CU1+ is being redefined. I'm not sure why such a molecule even exists in such a tutorial, but almost certainly you haven't followed the instructions as precisely as you needed to. If you don't understand how molecules get defined, have a read of the relevant part of chapter 5 of the manual. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] initial configuration problems and energy minimization
Arun kumar wrote: Dear gmx-users, Here I have a some problem regarding initial configuration My system is composed of cationic surfactants, co-surfactants, water. I am able to minimize the energy of my system(random), if it contains 15(surfactants)+ 15(co-surf)+ 1000(water)+ 15 (counterions) and also am able to simulate... But when I increase the number of surfactants or co-surfactants. Even the energy of the system initially is a big negative. When I start true simulation, Potential energy is becoming positive...and ultimately box is exploding [xtc error or some times ci error].. still I tried to minimize the energy of initial configuration, but I am getting the same error. Below I describe the steps i took to do simulations 1)minimize the energy of surfactnat(btm.gro)(includes counterion) and co-surfactant(str.gro) in Vaccum 2)Generate a system of 100 surfactnats(includes counterions), 20 co-surfactants and 1000 waters by using packmol(random) 3)Minimize the whole system until potential will become a reasonable negaive 4)With that minimized structure I run simulation but always the box is exploding My simulation is successful when the no of surf and co-surf are 15+15 For this successful simulation Initially i am conducting a NVT simulation with 0.01 fs timestep at 100K temp and then another NVT at desired temp(300K) and then NPT with 2fs timestep This looks pretty reasonable. You should check visually that packmol is not generating a conformation with atoms that are too close together. You can try using position restraints during your equilibration steps, and equilibrating for longer. The explosion is almost certainly happening because atoms are too close at some point, and these leads to huge energies. If your density is wrong for your NVT, then relaxing to NpT too quickly can cause this sort of problem too - use a large tau_t, or generate a box closer to the right size initially. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Calculate individual force between each atom pair
WU Yanbin wrote: Hi, Everyone, The force given by .trr file is the total force acted on each atom. Now I would like to modify codes to calculate individaul force between each atom pair. Is it possible in gromacs? (Because I remember some part of gromacs is writen in Fortran and already compiled). Err, no, not Fortran. The inner loops for calculating energies and forces are written in assembly for some common architectures, and there are fall-back routines in C. It would not be too hard to modify these C routines to write the nonbonded force between pairs of atoms in the inner loops. Writing that to output is likely to be unreasonably slow, and generate an unreasonably large data size (it's effectively a trajectory of size N^2 now). Depending on your application you might not need to write the numbers to a file, but you haven't told us what you want here. In any case, think very carefully about what you want to do, and then be prepared to understand the whole structure of mdrun, and lots of fine detail inside do_force() Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Compiling Gromacs on 64 bit windows platform...
Kedar Potdar wrote: I think, i forgot to mention that i am trying to compile GROMACS on native windows and not on Cygwin... That's going to make it hard to interest people in helping you, since probably nobody has done that before, and with the availability of cygwin few people have an incentive to do so. At the very least you could do a cygwin install and see how it constructs the Makefile... or just do a cygwin install and use it! :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to increase the number of
On 5/17/2007 8:14 PM, Afonso Duarte wrote: Dear All, I am using GROMACS 3.3.1 and i setup a simulation to run in 2 nodes of a workstation. It is running OK however now i have two extra nodes available to use in the same box and i would like to speed up the sim by using them. Is there any way to increase the number of nodes under use ? Check your MPICH/LAM implementation about how to boot up the extra nodes. I tried tpbconv to extend the sim and increase the np vaue but it did not worked. tpbconv cannot increase the nodes number. You have to opt for grompp, for which you can also obtain a exact continuation if you have .trr and .edr. Thanks Afonso __ Fale com seus amigos de graça com o novo Yahoo! Messenger http://br.messenger.yahoo.com/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] energy minimization - double precision
Dear users, I'm trying to minimize the energy of a protein in vacuum. I have restrained the backbone with posre.itp generated using genpr. when i try to minimize the energy of this protein using single precision grompp followed by an mdrun, it does not converge even after 600 steps and returns saying that it could not get to the requested minimum energy, and suggested that i use double precision for the same. so, i compiled gromacs with double precision and tried the same and i get the following. Could you help me solve this? Sometime back, venky wrote to the list that he would delete some atoms that clash. Considering i would not want to do that, could you suggest an alternative? the error i get is, Back Off! I just backed up wt_em.edr to ./#wt_em.edr.3# Low-Memory BFGS Minimizer: Tolerance (Fmax) = 1.0e+01 Number of steps= 50 Using 20 BFGS correction steps. F-max = inf on atom 1 F-Norm= inf Back Off! I just backed up wt_em.trr to ./#wt_em.trr.3# Step 0, Epot=-4.939505e+04, Fnorm= inf, Fmax= inf (atom 1) Step 1, Epot= nan, Fnorm= nan, Fmax=0.000e+00 (atom 0) writing lowest energy coordinates. Back Off! I just backed up wt_em.gro to ./#wt_em.gro.3# Low-Memory BFGS Minimizer converged to Fmax 10 in 1 steps Potential Energy = nan Maximum force = 0.00e+00 on atom 0 Norm of force = nan gcq#2: Jesus Built My Hotrod (Ministry) *** and this is my mdp file *** cpp = /lib/cpp define = -DPOSRES -DFLEX_SPC ; RUN CONTROL PARAMETERS integrator = l-bfgs tinit= 0 dt = 0.001 nsteps = 50 init_step= 0 comm-mode= Angular nstcomm = 1 comm-grps= ; LANGEVIN DYNAMICS OPTIONS bd-fric = 0 ld-seed = 1993 ; ENERGY MINIMIZATION OPTIONS emtol= 10 emstep = 0.001 nbfgscorr= 20 ; OUTPUT CONTROL OPTIONS nstxout = 1000 nstvout = 1000 nstfout = 0 nstcheckpoint= 1000 nstlog = 1000 nstenergy= 1000 nstxtcout= 0 xtc-precision= 100 xtc-grps = Protein energygrps = Protein ; NEIGHBORSEARCHING PARAMETERS nstlist = 1 ns-type = Simple pbc = no rlist= 1 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = Cut-off rcoulomb = 1 epsilon-r= 1 vdw-type = Cut-off rvdw-switch = 0 rvdw = 1 DispCorr = No ; OPTIONS FOR BONDS constraints = none constraint-algorithm = Lincs unconstrained-start = no lincs-order = 4 lincs-iter = 2 lincs-warnangle = 30 morse= no * thanks in advance, Kota. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] energy minimization - double precision
Pradeep Kota wrote: Dear users, I'm trying to minimize the energy of a protein in vacuum. I have restrained the backbone with posre.itp generated using genpr. when i try to minimize the energy of this protein using single precision grompp followed by an mdrun, it does not converge even after 600 steps and returns saying that it could not get to the requested minimum energy, and suggested that i use double precision for the same. so, i compiled gromacs with double precision and tried the same and i get the following. Could you help me solve this? Try a visual inspection of your structure before and after the single-precision minimization and look for sources of problems. You don't actually need convergence of minimization before an equilibration mdrun is a reasonable thing to try. Double precision minimization is only something you care about before (say) a normal-mode analysis. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] how to increase the number of
Oops ! am sorry. but i'm sure i had done this once earlier with some flag, without tinkering with the mdp file. i vaguely remember doing that. shall verify and get back to you. sorry afonso, and thanks for pointing out, mark ! :) regards, Kota. On 5/18/07, Mark Abraham [EMAIL PROTECTED] wrote: Pradeep Kota wrote: Hi Afonso, An easier way would be to use the -time flag with grompp. it would basically set the first time frame for the new tpr to what you give it. jus play around with it and i'm sure you can get what you wanted. dont forget to include the -np flag of course. :) No, that's not what grompp -time is for. See the man page. If you want to pretend it's the same simulation, by having the step numbering start from wherever you're up to, then there is an .mdp flag you can set. See section 7.3 of the manual. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] initial configuration problems and energy minimization
Hi Mark. Thanks for your suggestions I will use your suggestions to solve the problem. And then I will reply here about the outcomes. Regards Arun On 5/18/07, Mark Abraham [EMAIL PROTECTED] wrote: Arun kumar wrote: Dear gmx-users, Here I have a some problem regarding initial configuration My system is composed of cationic surfactants, co-surfactants, water. I am able to minimize the energy of my system(random), if it contains 15(surfactants)+ 15(co-surf)+ 1000(water)+ 15 (counterions) and also am able to simulate... But when I increase the number of surfactants or co-surfactants. Even the energy of the system initially is a big negative. When I start true simulation, Potential energy is becoming positive...and ultimately box is exploding [xtc error or some times ci error].. still I tried to minimize the energy of initial configuration, but I am getting the same error. Below I describe the steps i took to do simulations 1)minimize the energy of surfactnat(btm.gro)(includes counterion) and co-surfactant(str.gro) in Vaccum 2)Generate a system of 100 surfactnats(includes counterions), 20 co-surfactants and 1000 waters by using packmol(random) 3)Minimize the whole system until potential will become a reasonable negaive 4)With that minimized structure I run simulation but always the box is exploding My simulation is successful when the no of surf and co-surf are 15+15 For this successful simulation Initially i am conducting a NVT simulation with 0.01 fs timestep at 100K temp and then another NVT at desired temp(300K) and then NPT with 2fs timestep This looks pretty reasonable. You should check visually that packmol is not generating a conformation with atoms that are too close together. You can try using position restraints during your equilibration steps, and equilibrating for longer. The explosion is almost certainly happening because atoms are too close at some point, and these leads to huge energies. If your density is wrong for your NVT, then relaxing to NpT too quickly can cause this sort of problem too - use a large tau_t, or generate a box closer to the right size initially. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Arun kumar.V M.E Chemical ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] glibc error with g_density (only for some cases)
Dear gmx-users, I want to discuss and understand about an error I am getting only at times I am simulating a DPPC double bilayer phase(got the coordinates from Dr Tieleman's website). I used genbox -cs to get double bilayer. Then i started simulations normally. When I use g_density -b 500 I get the following error *** glibc detected *** free(): invalid next size (normal): 0x00713260 *** Aborted It is giving a empty density.xvg file I get same error if I use g_density -b 1000 I checked the reproducibility of the error.. I am getting it always(I mean I am using g_density once again again, Not simulating the system once again again) But when I use g_density -b 1500 or more I am getting densities normally. Actually i am doing simulations at 4 different temperatures. But I am getting the error only for three temperatures For one temperature Every thing is fine.. Gromacs version I am using is : 3.3.1 I checked the archives and in google I found a similar error in archives for make_ndx After checking in google I came to know that its a common bug with glibc package of different versions. Now i want to know is there anything wrong in my simulations(possibilities) and also how I can rid of these errors. Thanks and Regards -- Arun kumar.V M.E Chemical, IISc ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
