Re: [gmx-users] RE: optimizing the mailing list
Using emails, this might be done manually - each user will add to the TOPIC something like: tag install, etc`. Then each user could define his own rule, in his personal email account, how to deal with messages that contain tag xxx gromacs in the topic. Just a thought... Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Mon, Sep 8, 2008 at 21:17, David van der Spoel [EMAIL PROTECTED]wrote: Vitaly Chaban wrote: it's called internet forum... :) we've had this discussion before. On a forum many of the hardcore gromacs people (like me) would probably not respond anymore. I suggest that we consider ways in which the mailing list can be optimized. My initial thought is to allow submitters to flag messages as belonging to some particular topic(s). e.g. program crash force fields protein free energy coarse graining lipids and detergents unknown etc. Since the submission is by regular email and hence there is no possibility of introducing a radio box with topic options, this could be implemented by allowing any user to define the topic to which a particular message belongs. Ideally, the submitter would go to the website after submission and set the topic of their own submission. If the archives then allowed a user to view only a particular topic, then this would offer an alternative to the search tool, and also a link to such a topical list could be posted in the relevant pages on the wiki. I realize that the actual coding of such an interface may not be available at this time. But I suspect that somebody on this list knows some type of useful optimizations that are possible at this time. Chris. -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [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 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 convert gromacs traj file(.xtc) to amber traj file?
Are you sure this will be done automaticaly if you'll procide gromacs with an output file called filename.trj? There is also the option of converting into PDB: trjconv -f traj.xtc -o trajtraj.pdb -s coordinates.gro. omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Mon, Sep 8, 2008 at 20:14, ranqi zhu [EMAIL PROTECTED] wrote: Hi, Everyone, I just want to use the clustering tool in amber which only take trj file. Thanks -Ranqi -- Want to do more with Windows Live? Learn 10 hidden secrets from Jamie. Learn Nowhttp://windowslive.com/connect/post/jamiethomson.spaces.live.com-Blog-cns!550F681DAD532637!5295.entry?ocid=TXT_TAGLM_WL_domore_092008 ___ 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: Re: [gmx-users] sn1 and sn2 chains of popc
Thanks alot Justin for your detailed explanation. On Mon, 08 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Thanks Justin for your reply you mean to say that C32 of glycerol involves in the palimotyl chain formation so call as sn1 chain similarly C12,C13 of glycerol involves in the oleyl chain formation so call as sn2. Am I correct? More or less, let's just get a few things straight. Numbering like C32, C12, C13, etc. is a scheme devised to give sensible atomic numbering to all atoms in a 50 (or more)-atom lipid, but is not the same numbering scheme applied in conventional lipid numbering from Biochemistry lessons. To me, C32 has absolutely no bearing on sn-1. Look at the structure of glycerol: CH2OH | HO--C--H | CH2OH The second carbon is a chiral center, and (as I was taught in Biochemistry), that is where we derive the sn nomenclature: sn-2 = stereospecific number 2. The other carbons are given the obvious numbers of 1 and 3. By convention, the phosphate headgroup is assigned to carbon 3. Therefore, chain 1 is on the sn-1 carbon, and chain 2 is on sn-2. -Justin Thanks in advance. On Mon, 08 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Hi all, may be this is very basic query I want to calculate order parameters of popc. I have found in archives that make sn1.ndx(pamitoyl) and sn2.ndx(oleyl) of popc then feed these files to g_order command. Can anyone tell me that why pamitoyl call as sn1 and oleyl call as sn2? It derives from the numbering of the carbons on the glycerol backbone. -Justin Thanks for your help. 578x38_banner2.gif http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3OAS_QUERY=null ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin 578x38_banner2.gif http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3OAS_QUERY=null ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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] still some problems with HP-UX... grompp acting weird
Christopher Daub wrote: Hey again! The install of gromacs 3.3.3 on HP-UX is mostly working fine, but I'm getting some weird behaviour from grompp where it doesn't set the output filename correctly. Here is the grompp output from when I run the demo program, for example (the demo works fine until it gets to this step, after pdb2gmx and genbox): checking input for internal consistency... sh: /grace/bin/: Cannot create the specified file. grompp uses a temporary file and for the the environment variable $TMPDIR is read. Is that pointing to /grace/bin ? Cleaning up temporary file gromppa11751 --- Program grompp, VERSION 3.3.3 Source code file: topio.c, line: 312 Fatal error: Could not open /grace/bin/ --- If Life Seems Jolly Rotten, There's Something You've Forgotten ! (Monty Python ) :-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 3.3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: creating statusfile for 1 node... calling /usr/bin/cpp... cpp exit code: 256 Tried to execute: '/usr/local/bin/cpp -I/home/snoop/gmacs/share/gromacs/top -DFLEX_SP C cpeptide.top /grace/bin/' The '/usr/bin/cpp' command is defined in the .mdp file processing topology... - I think it's getting the /grace/bin thing from my PATH variable of all things! Why it sticks it in there as the output filename is beyond me. I've looked at grompp.c and topio.c to see if I can find the problem, but my C coding skills are not great and I'm not sure what to do with all those pointers... can anyone suggest an easy fix for this? I tried an ugly hack to set outfile = cppoutput in topio.c, but that didn't work... Thanks for any suggestions (other than getting rid of HP-UX...), Chris. ___ 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 van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [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] How to convert gromacs traj file(.xtc) to amber traj file?
Omer Markovitch wrote: Are you sure this will be done automaticaly if you'll procide gromacs with an output file called filename.trj? There is also the option of converting into PDB: trjconv -f traj.xtc -o trajtraj.pdb -s coordinates.gro. omer. try trjconv -o blabla.g87 -f something Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/ On Mon, Sep 8, 2008 at 20:14, ranqi zhu [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] wrote: Hi, Everyone, I just want to use the clustering tool in amber which only take trj file. Thanks -Ranqi Want to do more with Windows Live? Learn 10 hidden secrets from Jamie. Learn Now http://windowslive.com/connect/post/jamiethomson.spaces.live.com-Blog-cns!550F681DAD532637!5295.entry?ocid=TXT_TAGLM_WL_domore_092008 ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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] mailto:[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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [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] (no subject)
Hi all, I am interested about analyse some of the results with amber and gromacs md packages. Could anyone tell me how to convert .xtc of gromacs to trajectory input for amber. eagerly waiting for reply Thanks in advance.___ 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] conversion?
Hi all, I am interested about analyse some of the results with amber and gromacs md packages. Could anyone tell me how to convert .xtc of gromacs to trajectory input for amber. eagerly waiting for reply Thanks in advance.___ 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] Doubt in Energy minimization and Position restrained
Hi there, My apologies for asking question from basics. I have one doubt regarding order of Position restrained and Energy minimization. While running Position restrained, it soaks water molecule well within the protein molecule. In doing so on rearranging atoms it will again raise the energy of system (if I am not wrong). So, do we need to run Energy minimization again ? If not, then why ? With Thanks, Vivek ___ 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] Doubt in Energy minimization and Position restrained
vivek sharma wrote: Hi there, My apologies for asking question from basics. I have one doubt regarding order of Position restrained and Energy minimization. While running Position restrained, it soaks water molecule well within the protein molecule. In doing so on rearranging atoms it will again raise the energy of system (if I am not wrong). So, do we need to run Energy minimization again ? PR equilibration may or may not raise the energy. There is a pretty good chance that soaking in the solvent will establish more favorable water orientation (hydrogen bonding), thus potentially lowering the energy. There is no need to re-run EM after doing PR. Minimization simply provides a reasonable energetic starting point for the simulation, to avoid major steric clashes and unreasonable forces. Just because potential energy rises, doesn't mean the behavior is unreasonable. -Justin If not, then why ? With Thanks, Vivek ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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] conversion?
minnale wrote: Hi all, I am interested about analyse some of the results with amber and gromacs md packages. Could anyone tell me how to convert .xtc of gromacs to trajectory input for amber. eagerly waiting for reply The *exact* same question was asked yesterday: http://www.gromacs.org/pipermail/gmx-users/2008-September/036332.html ...with subsequent replies this morning. Do check the list archive for solutions, and keep an eye on (at least) the subject lines of the emails to the list. Every once in a while, one may come across that is of interest to you :) -Justin Thanks in advance. Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL PROTECTED]/2206641_2199021/2201650/1?PARTNER=3OAS_QUERY=null ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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: Re: [gmx-users] conversion?
thanks alot Justin for your reply On Tue, 09 Sep 2008 Justin A.Lemkul wrote : minnale wrote: Hi all, I am interested about analyse some of the results with amber and gromacs md packages. Could anyone tell me how to convert .xtc of gromacs to trajectory input for amber. eagerly waiting for reply The *exact* same question was asked yesterday: http://www.gromacs.org/pipermail/gmx-users/2008-September/036332.html ...with subsequent replies this morning. Do check the list archive for solutions, and keep an eye on (at least) the subject lines of the emails to the list. Every once in a while, one may come across that is of interest to you :) -Justin Thanks in advance. Rediff Shopping http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-home.htm/[EMAIL PROTECTED]/2206641_2199021/2201650/1?PARTNER=3OAS_QUERY=null ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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] g_dist
Hi all, I want to calculate distance of protein residues by using g_dist, now I have doubt that 1.Is it possible to calculate distance for more than two residues of two comparable systems? 2. which type of group select for generating index file?___ 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] g_dist
minnale wrote: Hi all, I want to calculate distance of protein residues by using g_dist, now I have doubt that 1.Is it possible to calculate distance for more than two residues of two comparable systems? g_dist calculates a simple center-of-mass distance between two points. What kind of distance are you trying to calculate that involves more than two points? 2. which type of group select for generating index file? That depends on what you want to analyze. If you select the whole residue, its center of mass will be used in the calculation. If you are more interested in specific functional groups interacting, perhaps you will want only those functional groups in the index file (or use g_mindist for a minimum distance between the residues). -Justin 578x38_banner2.gif http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/[EMAIL PROTECTED]/2606998_2599290/2602379/1?PARTNER=3OAS_QUERY=null ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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] 4.0_beta1: 1 particles communicated to PME node 9 are more than a cell length out of the domain decomposition cell of their charge group
Hi there, my system is about 200,000 atoms. we have installed the latest version (4.0_beta1) on our cluster but i get the follow error after few calculation ps : 1 particles communicated to PME node 9 are more than a cell length out of the domain decomposition cell of their charge group similar to what reported few months ago (http://www.gromacs.org/pipermail/gmx-revision/2008-July/000213.html). Using the version 3.3.99_development_200800503 on Louhi (csc.fi) the run goes fine. In our cluster with 4.0_beta1 i am using 36 cpus (with no -dd option) whereas on louhi 64 cpus (using -dd 4 4 4 option). I hope this help in gmx debugging Regards, andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 --- ___ 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] 4.0_beta1: 1 particles communicated to PME node 9 are more than a cell length out of the domain decomposition cell of their charge group
Hi again, in addition to the previous post, 4.0_beta1 crashes using 27 cpus and option -dd 3 3 3, whereas it goes fine using 24 cpus and not -dd option. any clue? Regards, andrea -- --- Andrea Spitaleri PhD Dulbecco Telethon Institute c/o DIBIT Scientific Institute Biomolecular NMR, 1B4 Via Olgettina 58 20132 Milano (Italy) http://biomolecularnmr.ihsr.dom/ Tel: 0039-0226434348/5622/3497/4922 Fax: 0039-0226434153 --- ___ 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] genion problem with large systems
Hi all, I'm experiencing a strange problem with genion that I have never seen before. I am preparing some membrane systems, many of which involve a large number of charged lipids (several hundred). When using lipids with PC headgroups (no net charge), the following works fine: genion -s ions.tpr -o system_solv_ions.gro -pname NA+ -nname CL- -neutral -conc 0.15 The only charged species is the embedded protein (-3 net charge). However, if I process a system containing, for example, 512 POPG lipids, genion (with the same command given above), always leaves the system with a net +2 charge. Even if I change -rmin (down to 0.1) or -seed, I get the same result, always a net +2. Obviously, I can fix this with another round of genion, but I was curious to see if there was some reason genion fails with the above command for systems with large numbers of charged species. I am using GMX 3.3.3. Thanks for your attention. -Justin -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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] still some problems with HP-UX... grompp acting weird
On Sep 9, 2008, at 2:53 AM, David van der Spoel wrote: Christopher Daub wrote: Hey again! The install of gromacs 3.3.3 on HP-UX is mostly working fine, but I'm getting some weird behaviour from grompp where it doesn't set the output filename correctly. Here is the grompp output from when I run the demo program, for example (the demo works fine until it gets to this step, after pdb2gmx and genbox): - --- checking input for internal consistency... sh: /grace/bin/: Cannot create the specified file. grompp uses a temporary file and for the the environment variable $TMPDIR is read. Is that pointing to /grace/bin ? Thanks a lot for the suggestion. This variable is not set. I tried to set it to the current directory (export TMPDIR=./), but it didn't make a difference. Where is this set? I grep'd for TMPDIR in the src/ kernel directory and couldn't find any reference to it... are you sure this is right? Maybe there's another variable getting set somewhere... is there a list somewhere of environment variables used by gromacs? I tried other preprocessors other than the default cpp (m4, and a cpp.ansi I found in /usr/lib) but get the same error... so it does seem to be grompp, not the cpp... Cheers, Chris. Cleaning up temporary file gromppa11751 --- Program grompp, VERSION 3.3.3 Source code file: topio.c, line: 312 Fatal error: Could not open /grace/bin/ --- If Life Seems Jolly Rotten, There's Something You've Forgotten ! (Monty Python ) :-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 3.3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: creating statusfile for 1 node... calling /usr/bin/cpp... cpp exit code: 256 Tried to execute: '/usr/local/bin/cpp -I/home/snoop/gmacs/share/ gromacs/top -DFLEX_SP C cpeptide.top /grace/bin/' The '/usr/bin/cpp' command is defined in the .mdp file processing topology... - I think it's getting the /grace/bin thing from my PATH variable of all things! Why it sticks it in there as the output filename is beyond me. I've looked at grompp.c and topio.c to see if I can find the problem, but my C coding skills are not great and I'm not sure what to do with all those pointers... can anyone suggest an easy fix for this? I tried an ugly hack to set outfile = cppoutput in topio.c, but that didn't work... Thanks for any suggestions (other than getting rid of HP-UX...), Chris. ___ 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 van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [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 the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] still some problems with HP-UX... grompp acting weird
Christopher Daub wrote: On Sep 9, 2008, at 2:53 AM, David van der Spoel wrote: Christopher Daub wrote: Hey again! The install of gromacs 3.3.3 on HP-UX is mostly working fine, but I'm getting some weird behaviour from grompp where it doesn't set the output filename correctly. Here is the grompp output from when I run the demo program, for example (the demo works fine until it gets to this step, after pdb2gmx and genbox): checking input for internal consistency... sh: /grace/bin/: Cannot create the specified file. grompp uses a temporary file and for the the environment variable $TMPDIR is read. Is that pointing to /grace/bin ? try running the programs outside the demo script. In the worst case you can run grompp on another box, and only use mdrun on the HP. Thanks a lot for the suggestion. This variable is not set. I tried to set it to the current directory (export TMPDIR=./), but it didn't make a difference. Where is this set? I grep'd for TMPDIR in the src/kernel directory and couldn't find any reference to it... are you sure this is right? Maybe there's another variable getting set somewhere... is there a list somewhere of environment variables used by gromacs? I tried other preprocessors other than the default cpp (m4, and a cpp.ansi I found in /usr/lib) but get the same error... so it does seem to be grompp, not the cpp... Cheers, Chris. Cleaning up temporary file gromppa11751 --- Program grompp, VERSION 3.3.3 Source code file: topio.c, line: 312 Fatal error: Could not open /grace/bin/ --- If Life Seems Jolly Rotten, There's Something You've Forgotten ! (Monty Python ) :-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 3.3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: creating statusfile for 1 node... calling /usr/bin/cpp... cpp exit code: 256 Tried to execute: '/usr/local/bin/cpp -I/home/snoop/gmacs/share/gromacs/top -DFLEX_SP C cpeptide.top /grace/bin/' The '/usr/bin/cpp' command is defined in the .mdp file processing topology... - I think it's getting the /grace/bin thing from my PATH variable of all things! Why it sticks it in there as the output filename is beyond me. I've looked at grompp.c and topio.c to see if I can find the problem, but my C coding skills are not great and I'm not sure what to do with all those pointers... can anyone suggest an easy fix for this? I tried an ugly hack to set outfile = cppoutput in topio.c, but that didn't work... Thanks for any suggestions (other than getting rid of HP-UX...), Chris. ___ 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 van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. [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 -- David van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of
[gmx-users] I invite you to see MyDailyFlog page!
Hi! I would like to invite you to visit MyDailyFlog and see my latest photos. Check out: http://www.mydailyflog.com/sunitabioinfo Cheers! sunita gupta Got a digital camera? MyDailyFlog is a personal photo-blogging space where you can easily post your latest and greatest photos, and share them with your friends and family. Create your own DailyFlog at www.MyDailyFlog.com ... Unsubscribe: to opt out of further invitations from your friends to see their DailyFlogs, please click below: http://www.mydailyflog.com/go/system/[EMAIL PROTECTED]md5=0a7446578d52aea5ff088f5b5515c0b8 Please do not reply directly to this email. Questions? Contact us - http://www.mydailyflog.com/go/contact_us MyDailyFlog, Refriendz Ltd. PO BOX 1184, Luton, Bedfordshire, LU1 9AT. ___ 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] D2O
Hi Does Gromacs support D2O simulation? Is it any difference between the D2O and H2O except the molecular weight? and, how about the force field parameters? are the two systems just the same? Thank you Lin ___ 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] D2O
Chih-Ying Lin wrote: Hi Does Gromacs support D2O simulation? Is it any difference between the D2O and H2O except the molecular weight? and, how about the force field parameters? are the two systems just the same? If you have a flexible model you would have to change the force constants, for a rigid model it is the same except for the masses. There is also pdb2gmx -deuterate (for proteins...) Thank you Lin ___ 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 van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [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] still some problems with HP-UX... grompp acting weird
On Sep 9, 2008, at 12:43 PM, David van der Spoel wrote: Christopher Daub wrote: On Sep 9, 2008, at 2:53 AM, David van der Spoel wrote: Christopher Daub wrote: Hey again! The install of gromacs 3.3.3 on HP-UX is mostly working fine, but I'm getting some weird behaviour from grompp where it doesn't set the output filename correctly. Here is the grompp output from when I run the demo program, for example (the demo works fine until it gets to this step, after pdb2gmx and genbox): --- - checking input for internal consistency... sh: /grace/bin/: Cannot create the specified file. grompp uses a temporary file and for the the environment variable $TMPDIR is read. Is that pointing to /grace/bin ? try running the programs outside the demo script. Yep, tried that... makes no difference. I've tried a different HP box, and another user also tried, in which case, the attempted output directory is a different mangled piece of our respective $PATH variables. Every attempt to run grompp does the same weird thing. In the worst case you can run grompp on another box, and only use mdrun on the HP. Thanks, we may have to do that... but will it work? grompp will make a binary .tpr file, I don't think I'll be able to read that with mdrun running somewhere else, or will I? Thanks again, Chris. Thanks a lot for the suggestion. This variable is not set. I tried to set it to the current directory (export TMPDIR=./), but it didn't make a difference. Where is this set? I grep'd for TMPDIR in the src/kernel directory and couldn't find any reference to it... are you sure this is right? Maybe there's another variable getting set somewhere... is there a list somewhere of environment variables used by gromacs? I tried other preprocessors other than the default cpp (m4, and a cpp.ansi I found in /usr/lib) but get the same error... so it does seem to be grompp, not the cpp... Cheers, Chris. Cleaning up temporary file gromppa11751 --- Program grompp, VERSION 3.3.3 Source code file: topio.c, line: 312 Fatal error: Could not open /grace/bin/ --- If Life Seems Jolly Rotten, There's Something You've Forgotten ! (Monty Python ) :-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 3.3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: creating statusfile for 1 node... calling /usr/bin/cpp... cpp exit code: 256 Tried to execute: '/usr/local/bin/cpp -I/home/snoop/gmacs/share/ gromacs/top -DFLEX_SP C cpeptide.top /grace/bin/' The '/usr/bin/cpp' command is defined in the .mdp file processing topology... - I think it's getting the /grace/bin thing from my PATH variable of all things! Why it sticks it in there as the output filename is beyond me. I've looked at grompp.c and topio.c to see if I can find the problem, but my C coding skills are not great and I'm not sure what to do with all those pointers... can anyone suggest an easy fix for this? I tried an ugly hack to set outfile = cppoutput in topio.c, but that didn't work... Thanks for any suggestions (other than getting rid of HP-UX...), Chris. ___ 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 van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. [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
Re: [gmx-users] still some problems with HP-UX... grompp acting weird
Christopher Daub wrote: On Sep 9, 2008, at 12:43 PM, David van der Spoel wrote: Christopher Daub wrote: On Sep 9, 2008, at 2:53 AM, David van der Spoel wrote: Christopher Daub wrote: Hey again! The install of gromacs 3.3.3 on HP-UX is mostly working fine, but I'm getting some weird behaviour from grompp where it doesn't set the output filename correctly. Here is the grompp output from when I run the demo program, for example (the demo works fine until it gets to this step, after pdb2gmx and genbox): checking input for internal consistency... sh: /grace/bin/: Cannot create the specified file. grompp uses a temporary file and for the the environment variable $TMPDIR is read. Is that pointing to /grace/bin ? try running the programs outside the demo script. Yep, tried that... makes no difference. I've tried a different HP box, and another user also tried, in which case, the attempted output directory is a different mangled piece of our respective $PATH variables. Every attempt to run grompp does the same weird thing. I'm afraid this is going to be hard to reproduce because as far as I know neither of the developers has a HPUX system. It sounds like a problem in the getenv C-library function... In the worst case you can run grompp on another box, and only use mdrun on the HP. Thanks, we may have to do that... but will it work? grompp will make a binary .tpr file, I don't think I'll be able to read that with mdrun running somewhere else, or will I? Yes, these files are portable. Thanks again, Chris. Thanks a lot for the suggestion. This variable is not set. I tried to set it to the current directory (export TMPDIR=./), but it didn't make a difference. Where is this set? I grep'd for TMPDIR in the src/kernel directory and couldn't find any reference to it... are you sure this is right? Maybe there's another variable getting set somewhere... is there a list somewhere of environment variables used by gromacs? I tried other preprocessors other than the default cpp (m4, and a cpp.ansi I found in /usr/lib) but get the same error... so it does seem to be grompp, not the cpp... Cheers, Chris. Cleaning up temporary file gromppa11751 --- Program grompp, VERSION 3.3.3 Source code file: topio.c, line: 312 Fatal error: Could not open /grace/bin/ --- If Life Seems Jolly Rotten, There's Something You've Forgotten ! (Monty Python ) :-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 3.3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: creating statusfile for 1 node... calling /usr/bin/cpp... cpp exit code: 256 Tried to execute: '/usr/local/bin/cpp -I/home/snoop/gmacs/share/gromacs/top -DFLEX_SP C cpeptide.top /grace/bin/' The '/usr/bin/cpp' command is defined in the .mdp file processing topology... - I think it's getting the /grace/bin thing from my PATH variable of all things! Why it sticks it in there as the output filename is beyond me. I've looked at grompp.c and topio.c to see if I can find the problem, but my C coding skills are not great and I'm not sure what to do with all those pointers... can anyone suggest an easy fix for this? I tried an ugly hack to set outfile = cppoutput in topio.c, but that didn't work... Thanks for any suggestions (other than getting rid of HP-UX...), Chris. ___ 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 van der Spoel, Ph.D., Professor of Biology Molec. Biophys. group, Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone:+46184714205. Fax: +4618511755. [EMAIL PROTECTED][EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org
[gmx-users] trjconv
Dear Users, I have a question about the option -fit in trjconv. The default option with -fit is none. If I use the option as rot+trans, does it mean that the rotational and translational motions are removed from the trajectory ? If not, is there any option in gromacs, to create a translational and rotational free trajectory from the original trajecotry file ? I also want to make sure the usage of the command: trjconv -f original trr -s .tpr -o rot_trans_free.trr -fit rot+trans Thanks in advance. Ram. ___ 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] still some problems with HP-UX... grompp acting weird
On Sep 9, 2008, at 3:31 PM, David van der Spoel wrote: Christopher Daub wrote: On Sep 9, 2008, at 12:43 PM, David van der Spoel wrote: Christopher Daub wrote: On Sep 9, 2008, at 2:53 AM, David van der Spoel wrote: Christopher Daub wrote: Hey again! The install of gromacs 3.3.3 on HP-UX is mostly working fine, but I'm getting some weird behaviour from grompp where it doesn't set the output filename correctly. Here is the grompp output from when I run the demo program, for example (the demo works fine until it gets to this step, after pdb2gmx and genbox): - --- checking input for internal consistency... sh: /grace/bin/: Cannot create the specified file. grompp uses a temporary file and for the the environment variable $TMPDIR is read. Is that pointing to /grace/bin ? try running the programs outside the demo script. Yep, tried that... makes no difference. I've tried a different HP box, and another user also tried, in which case, the attempted output directory is a different mangled piece of our respective $PATH variables. Every attempt to run grompp does the same weird thing. I'm afraid this is going to be hard to reproduce because as far as I know neither of the developers has a HPUX system. It sounds like a problem in the getenv C-library function... Hmm. getenv seems to work elsewhere in the codes (finding $GMXLIB etc)... I wonder why it messes up here? Maybe I could compile grompp with lower optimization, or with gcc instead of the HP compilers... I'll try that sometime. In the worst case you can run grompp on another box, and only use mdrun on the HP. Thanks, we may have to do that... but will it work? grompp will make a binary .tpr file, I don't think I'll be able to read that with mdrun running somewhere else, or will I? Yes, these files are portable. OK, I tried this and it does work. Thanks! For now I guess this will be our M.O... Thanks again for all the help, Chris. Thanks again, Chris. Thanks a lot for the suggestion. This variable is not set. I tried to set it to the current directory (export TMPDIR=./), but it didn't make a difference. Where is this set? I grep'd for TMPDIR in the src/kernel directory and couldn't find any reference to it... are you sure this is right? Maybe there's another variable getting set somewhere... is there a list somewhere of environment variables used by gromacs? I tried other preprocessors other than the default cpp (m4, and a cpp.ansi I found in /usr/lib) but get the same error... so it does seem to be grompp, not the cpp... Cheers, Chris. Cleaning up temporary file gromppa11751 --- Program grompp, VERSION 3.3.3 Source code file: topio.c, line: 312 Fatal error: Could not open /grace/bin/ --- If Life Seems Jolly Rotten, There's Something You've Forgotten ! (Monty Python ) :-) G R O M A C S (-: GRoups of Organic Molecules in ACtion for Science :-) VERSION 3.3.3 (-: Written by David van der Spoel, Erik Lindahl, Berk Hess, and others. Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2008, The GROMACS development team, check out http://www.gromacs.org for more information. This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. :-) grompp (-: creating statusfile for 1 node... calling /usr/bin/cpp... cpp exit code: 256 Tried to execute: '/usr/local/bin/cpp -I/home/snoop/gmacs/ share/gromacs/top -DFLEX_SP C cpeptide.top /grace/bin/' The '/usr/bin/cpp' command is defined in the .mdp file processing topology... - I think it's getting the /grace/bin thing from my PATH variable of all things! Why it sticks it in there as the output filename is beyond me. I've looked at grompp.c and topio.c to see if I can find the problem, but my C coding skills are not great and I'm not sure what to do with all those pointers... can anyone suggest an easy fix for this? I tried an ugly hack to set outfile = cppoutput in topio.c, but that didn't work... Thanks for any suggestions (other than getting rid of HP-UX...), Chris. ___ 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
[gmx-users] OPLS force field does not recognize Atom type
Dear I want to make the solution which is not working with unified atom force fields. Then I decided to make the itp file by my own. I made the all atom type itp file for opls AA. I found all of the opls feature in gromacs top directory and according to the top directory files I made the new itp file. Unfortunately, after running the grompp i faced with the following error: Fatal error: Atomtype 'HC' not found! but it is defined in the opls. My itp file structure is like follow: ; [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1HC 1 DRG HAD 10.02734 1.0080 2CT 1 DRG CAL 10.10638 12.0110 3HC 1 DRG HAE 10.02734 1.0080 4OS 1 DRG OAI 1 -0.36111 15.9994 5CT 1 DRG CAK 10.10638 12.0110 6HC 1 DRG HAB 20.02734 1.0080 7HC 1 DRG HAG 20.02734 1.0080 8CY 1 DRG CAM 20.00235 12.0110 9HC 1 DRG HAF 30.00857 1.0080 10HC 1 DRG HAH 30.00857 1.0080 11CY 1 DRG CAJ 30.00235 12.0110 12HC 1 DRG HAC 30.00857 1.0080 13HC 1 DRG HAA 30.00857 1.0080 [ bonds ] ; ai aj fuc0, c1, ... 1 2 10.109284512.00.109284512.0 ; HAD CAL 2 3 10.109284512.00.109284512.0 ; CAL HAE 2 4 10.141267776.00.141267776.0 ; CAL HAI 2 11 10.152217568.00.152217568.0 ; CAL CAJ 4 5 10.141267776.00.141267776.0 ; OAI CAK 5 6 10.109284512.00.109284512.0 ; CAK HAB 5 7 10.109284512.00.109284512.0 ; CAK HAG 5 8 10.151234304.00.151234304.0 ; CAK CAM 8 9 10.108284512.00.108284512.0 ; CAM HAF 8 10 10.108284512.00.108284512.0 ; CAM HAH 8 11 10.150217568.00.150217568.0 ; CAM CAJ 11 12 10.108284512.00.108284512.0 ; CAJ HAC 11 13 10.108284512.00.108284512.0 ; CAJ HAA [ pairs ] ; ai aj fuc0, c1, ... 1 5 1 ; HAD CAK 1 8 1 ; HAD CAM 1 12 1 ; HAD HAC 1 13 1 ; HAD HAA 2 6 1 ; CAL HAB 2 7 1 ; CAL HAG 2 9 1 ; CAL HAF 2 10 1 ; CAL HAH 3 5 1 ; HAE CAK 3 8 1 ; HAE CAM 3 12 1 ; HAE HAC 6 9 1 ; HAB HAF 8 10 1 ; HAB HAH 6 11 1 ; HAB CAJ 7 9 1 ; HAG HAF 7 10 1 ; HAG HAH 7 11 1 ; HAG CAJ 9 12 1 ; HAF HAC 9 13 1 ; HAF HAA 10 12 1 ; HAH HAC 10 13 1 ; HAH HAA [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 1107.8 276.1107.8 276.1 ; HAD CAL HAE 1 2 4 1109.5 292.8109.5 292.8 ; HAD CAL OAI 1 2 11 1110.7 313.8109.5 397.5 ; HAD CAL CAJ 3 2 4 1109.5 292.8109.5 292.8 ; HAE CAL OAI 3 2 11 1110.7 313.8110.7 313.8 ; HAE CAL CAJ 4 2 11 1109.5 292.8109.5 292.8 ; OAI CAL CAJ 2 4 5 1109.5 502.0109.5 502.0 ; CAL OAI CAK 4 5 6 1109.5 292.8109.5 292.8 ; OAI CAK HAB 4 5 7 1109.5 292.8109.5 292.8 ; OAI CAK HAG 4 5 8 1109.5 292.8109.5 292.8 ; OAI CAK CAM 6 5 7 1107.8 276.1107.8 276.1 ; HAB CAK HAG 6 5 8 1110.7 313.8110.7 313.8 ; HAB CAK CAM 7 5 8 1110.7 313.8110.7 313.8 ; HAG CAK CAM 5 8 9 1114.3 292.8114.3 292.8 ; CAK CAM HAF 5 8 10 1114.3 292.8114.3
Re: [gmx-users] OPLS force field does not recognize Atom type
Morteza Khabiri wrote: Dear I want to make the solution which is not working with unified atom force fields. Then I decided to make the itp file by my own. I made the all atom type itp file for opls AA. I found all of the opls feature in gromacs top directory and according to the top directory files I made the new itp file. Unfortunately, after running the grompp i faced with the following error: Fatal error: Atomtype 'HC' not found! but it is defined in the opls. How so? If you look in ffoplsaa.atp, you will note that all atomtypes are defined as opls_XXX. -Justin My itp file structure is like follow: ; [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1HC 1 DRG HAD 10.02734 1.0080 2CT 1 DRG CAL 10.10638 12.0110 3HC 1 DRG HAE 10.02734 1.0080 4OS 1 DRG OAI 1 -0.36111 15.9994 5CT 1 DRG CAK 10.10638 12.0110 6HC 1 DRG HAB 20.02734 1.0080 7HC 1 DRG HAG 20.02734 1.0080 8CY 1 DRG CAM 20.00235 12.0110 9HC 1 DRG HAF 30.00857 1.0080 10HC 1 DRG HAH 30.00857 1.0080 11CY 1 DRG CAJ 30.00235 12.0110 12HC 1 DRG HAC 30.00857 1.0080 13HC 1 DRG HAA 30.00857 1.0080 [ bonds ] ; ai aj fuc0, c1, ... 1 2 10.109284512.00.109284512.0 ; HAD CAL 2 3 10.109284512.00.109284512.0 ; CAL HAE 2 4 10.141267776.00.141267776.0 ; CAL HAI 2 11 10.152217568.00.152217568.0 ; CAL CAJ 4 5 10.141267776.00.141267776.0 ; OAI CAK 5 6 10.109284512.00.109284512.0 ; CAK HAB 5 7 10.109284512.00.109284512.0 ; CAK HAG 5 8 10.151234304.00.151234304.0 ; CAK CAM 8 9 10.108284512.00.108284512.0 ; CAM HAF 8 10 10.108284512.00.108284512.0 ; CAM HAH 8 11 10.150217568.00.150217568.0 ; CAM CAJ 11 12 10.108284512.00.108284512.0 ; CAJ HAC 11 13 10.108284512.00.108284512.0 ; CAJ HAA [ pairs ] ; ai aj fuc0, c1, ... 1 5 1 ; HAD CAK 1 8 1 ; HAD CAM 1 12 1 ; HAD HAC 1 13 1 ; HAD HAA 2 6 1 ; CAL HAB 2 7 1 ; CAL HAG 2 9 1 ; CAL HAF 2 10 1 ; CAL HAH 3 5 1 ; HAE CAK 3 8 1 ; HAE CAM 3 12 1 ; HAE HAC 6 9 1 ; HAB HAF 8 10 1 ; HAB HAH 6 11 1 ; HAB CAJ 7 9 1 ; HAG HAF 7 10 1 ; HAG HAH 7 11 1 ; HAG CAJ 9 12 1 ; HAF HAC 9 13 1 ; HAF HAA 10 12 1 ; HAH HAC 10 13 1 ; HAH HAA [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 1107.8 276.1107.8 276.1 ; HAD CAL HAE 1 2 4 1109.5 292.8109.5 292.8 ; HAD CAL OAI 1 2 11 1110.7 313.8109.5 397.5 ; HAD CAL CAJ 3 2 4 1109.5 292.8109.5 292.8 ; HAE CAL OAI 3 2 11 1110.7 313.8110.7 313.8 ; HAE CAL CAJ 4 2 11 1109.5 292.8109.5 292.8 ; OAI CAL CAJ 2 4 5 1109.5 502.0109.5 502.0 ; CAL OAI CAK 4 5 6 1109.5 292.8109.5 292.8 ; OAI CAK HAB 4 5 7 1109.5 292.8109.5 292.8 ; OAI CAK HAG 4 5 8 1109.5 292.8109.5 292.8 ; OAI CAK CAM 6 5 7 1107.8 276.1107.8 276.1 ; HAB CAK HAG 6 5 8 1110.7 313.8110.7 313.8 ; HAB CAK CAM 7 5 8 1110.7 313.8110.7 313.8 ; HAG CAK
Re: [gmx-users] OPLS force field does not recognize Atom type
* Morteza Khabiri [EMAIL PROTECTED] [2008-09-09 22:03:36 +0200]: Dear I want to make the solution which is not working with unified atom force fields. Then I decided to make the itp file by my own. I made the all atom type itp file for opls AA. I found all of the opls feature in gromacs top directory and according to the top directory files I made the new itp file. Unfortunately, after running the grompp i faced with the following error: Fatal error: Atomtype 'HC' not found! but it is defined in the opls. My itp file structure is like follow: ; [ moleculetype ] ; Name nrexcl DRG 3 [ atoms ] ; nr type resnr resid atom cgnr charge mass 1HC 1 DRG HAD 10.02734 1.0080 2CT 1 DRG CAL 10.10638 12.0110 Hello, your faulty itp file results from the string in the second column. It should correspond to the OPLS atom nr, like opls_032. Best Regards, Flo 3HC 1 DRG HAE 10.02734 1.0080 4OS 1 DRG OAI 1 -0.36111 15.9994 5CT 1 DRG CAK 10.10638 12.0110 6HC 1 DRG HAB 20.02734 1.0080 7HC 1 DRG HAG 20.02734 1.0080 8CY 1 DRG CAM 20.00235 12.0110 9HC 1 DRG HAF 30.00857 1.0080 10HC 1 DRG HAH 30.00857 1.0080 11CY 1 DRG CAJ 30.00235 12.0110 12HC 1 DRG HAC 30.00857 1.0080 13HC 1 DRG HAA 30.00857 1.0080 [ bonds ] ; ai aj fuc0, c1, ... 1 2 10.109284512.00.109284512.0 ; HAD CAL 2 3 10.109284512.00.109284512.0 ; CAL HAE 2 4 10.141267776.00.141267776.0 ; CAL HAI 2 11 10.152217568.00.152217568.0 ; CAL CAJ 4 5 10.141267776.00.141267776.0 ; OAI CAK 5 6 10.109284512.00.109284512.0 ; CAK HAB 5 7 10.109284512.00.109284512.0 ; CAK HAG 5 8 10.151234304.00.151234304.0 ; CAK CAM 8 9 10.108284512.00.108284512.0 ; CAM HAF 8 10 10.108284512.00.108284512.0 ; CAM HAH 8 11 10.150217568.00.150217568.0 ; CAM CAJ 11 12 10.108284512.00.108284512.0 ; CAJ HAC 11 13 10.108284512.00.108284512.0 ; CAJ HAA [ pairs ] ; ai aj fuc0, c1, ... 1 5 1 ; HAD CAK 1 8 1 ; HAD CAM 1 12 1 ; HAD HAC 1 13 1 ; HAD HAA 2 6 1 ; CAL HAB 2 7 1 ; CAL HAG 2 9 1 ; CAL HAF 2 10 1 ; CAL HAH 3 5 1 ; HAE CAK 3 8 1 ; HAE CAM 3 12 1 ; HAE HAC 6 9 1 ; HAB HAF 8 10 1 ; HAB HAH 6 11 1 ; HAB CAJ 7 9 1 ; HAG HAF 7 10 1 ; HAG HAH 7 11 1 ; HAG CAJ 9 12 1 ; HAF HAC 9 13 1 ; HAF HAA 10 12 1 ; HAH HAC 10 13 1 ; HAH HAA [ angles ] ; ai aj ak fuc0, c1, ... 1 2 3 1107.8 276.1107.8 276.1 ; HAD CAL HAE 1 2 4 1109.5 292.8109.5 292.8 ; HAD CAL OAI 1 2 11 1110.7 313.8109.5 397.5 ; HAD CAL CAJ 3 2 4 1109.5 292.8109.5 292.8 ; HAE CAL OAI 3 2 11 1110.7 313.8110.7 313.8 ; HAE CAL CAJ 4 2 11 1109.5 292.8109.5 292.8 ; OAI CAL CAJ 2 4 5 1109.5 502.0109.5 502.0 ; CAL OAI CAK 4 5 6 1109.5 292.8109.5 292.8 ; OAI CAK HAB 4 5 7 1109.5 292.8109.5 292.8 ; OAI CAK HAG 4 5 8 1109.5 292.8109.5 292.8 ; OAI CAK CAM 6 5 7 1107.8 276.1107.8 276.1 ; HAB CAK HAG 6 5 8 1110.7 313.8110.7 313.8 ; HAB CAK CAM 7 5 8 1110.7 313.8
[gmx-users] fatal errors regarding grid cells
Hi, I am getting this error number of times when I am trying to run Md with a 9 residue peptide in water box using spc216.gro It says Number of grid cells is zero. Probably the system and box collapsed. earlier after grompp it gives me warning that the protein atom number is less than 10% of total atom number. I dont know if that is causing any problem. even if I change ns_type in .mdp file to simple from grid, the problem persists. Please help. Thanks and regards, Subhashis ___ 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] fatal errors regarding grid cells
NAMD GROMACS wrote: Hi, I am getting this error number of times when I am trying to run Md with a 9 residue peptide in water box using spc216.gro It says Number of grid cells is zero. Probably the system and box collapsed. earlier after grompp it gives me warning that the protein atom number is less than 10% of total atom number. I dont know if that is causing any problem. even if I change ns_type in .mdp file to simple from grid, the problem persists. Have you searched the mailing list archives? If you search number of grid cells is zero, you return 70 posts! Probably one of them will have a clue. The reason I say this is that you've provided no pertinent details of your system - what it contains, how (and if) you prepared, minimized, and equilibrated your system. -Justin Please help. Thanks and regards, Subhashis ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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] D2O
Hi I would like to simulate the solutes are embeded in D2O solution. Could someone explain the difference of simulating D2O solution and H2O solution? Thank you Lin ___ 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] D2O
Well, from a simulation standpoint these systems are usually regarded as having identical structures at a classical level; the dynamics are a bit slower due to the heavier D vs. H, but this does not affect the solution structure. The force fields are identical except for the heavier mass. However, in reality this isn't quite true... there is evidence from neutron diffraction (see some of Alan Soper's work) that the structures of D2O and H2O are a bit different, and this should be reflected in slight differences in the potential model of D2O. But you will probably have to look around and do some work yourself to find/develop a good D2O potential, if you want to investigate the isotope dependence. I'm pretty sure there is no well-determined, official literature value for this! Good luck, Chris. On Sep 9, 2008, at 6:11 PM, Chih-Ying Lin wrote: Hi I would like to simulate the solutes are embeded in D2O solution. Could someone explain the difference of simulating D2O solution and H2O solution? Thank you Lin ___ 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] OPLS force field does not recognize Atom type
Dear As you said I change the name of the itp file to opls_xxx. It works. thank you very much. But now i faced with new problem. I got new error: Fatal error: Incorrect number of parameters - found 4, expected 6 or 12. what does it mean? Thank you in advance Morteza ___ 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] D2O
Hi Chih-Ying Lin, besides supporting Christophers general comments, I would just add that there actually are D2O models available in literature: An effective pair potential for heavy water J.Chem.Phys. (2001) v. 114, Issue 18, pp. 8064-8067. I would also like to point you in the direction of a previous discussion on the list addressing this same topic. A D2O gromacs mailing lists query will produce (among others) the following results which might be of assistance to you: [gmx-users] Topology file for D2O Location: http://www.gromacs.org/pipermail/gmx-users/2007-March/026569.html Cheers, Andrés PS: I believe I still have the modified FF files + D2O topology (derived from the reference) if you should need them. Christopher Daub [EMAIL PROTECTED] ha escrito: Well, from a simulation standpoint these systems are usually regarded as having identical structures at a classical level; the dynamics are a bit slower due to the heavier D vs. H, but this does not affect the solution structure. The force fields are identical except for the heavier mass. However, in reality this isn't quite true... there is evidence from neutron diffraction (see some of Alan Soper's work) that the structures of D2O and H2O are a bit different, and this should be reflected in slight differences in the potential model of D2O. But you will probably have to look around and do some work yourself to find/develop a good D2O potential, if you want to investigate the isotope dependence. I'm pretty sure there is no well-determined, official literature value for this! Good luck, Chris. On Sep 9, 2008, at 6:11 PM, Chih-Ying Lin wrote: Hi I would like to simulate the solutes are embeded in D2O solution. Could someone explain the difference of simulating D2O solution and H2O solution? Thank you Lin ___ 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 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. This message was sent using IMP, the Internet Messaging Program. -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. ___ 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] OPLS force field does not recognize Atom type
Morteza Khabiri wrote: Dear As you said I change the name of the itp file to opls_xxx. It works. thank you very much. But now i faced with new problem. I got new error: Fatal error: Incorrect number of parameters - found 4, expected 6 or 12. It was probably printed with a line number in the topology. What you need to do is identify what parameter that corresponds to, then read in Chapter 5 of the manual about what types of parameters you need to specify. -Justin what does it mean? Thank you in advance Morteza ___ 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 -- Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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
