RE: [gmx-users] itp for alamethicin
Good place to have a read is: http://wiki.gromacs.org/index.php/Category:Force_Fields Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ 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] itp for alamethicin
pragya chohan wrote: hi... i have to make an itp file for alamethicin already tried prodrg2 but no success. pls suggest a way for making .itp file .. residue already defined in ffgmx.rtp. ...already read earlier query posted but could not find an ans. pls rite norml Engspeak in full sentses Try contacting Peter Tieleman and asking for the topology. He has posted many pdbs for alamethicin on his groups website: http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies You can find his email address here: http://moose.bio.ucalgary.ca/index.php?page=Peter_Tieleman http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation 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] itp for alamethicin
pragya chohan wrote: hi... i have to make an itp file for alamethicin already tried prodrg2 but no success. pls suggest a way for making .itp file .. residue already defined in ffgmx.rtp. ...already read earlier query posted but could not find an ans. pls rite norml Engspeak in full sentses http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation 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 are you
[EMAIL PROTECTED] wrote: Sir: How are you! I am a new user of gmx.At first,sincere tribute to you and all the gmx developers! I want to perform a molecular dynamics simulation on the tobramycin aqueous soluton by gmx. On the simulation process,I encounter some problem and I can't treat with it by myself and I hope you will give me a hand. Tobramycin is a aminoglycosidic substance, Its pdb file is not availabe in the PDB bank, so I generate it with a comercial software Material studio. but it is not in consistent with gmx command of pdb2gmx. More information is needed in order to actually help you. I want to know how can I deal with it and it the other way to generate a pdb file of tobramycin in gmx format. Well-formed PDB *is* accepted by GROMACS. At the same time, how to obtain the parameter of tobramycin in gmx opls format? Start at the beginning... see http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation 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] itp for alamethicin
hi... i have to make an itp file for alamethicin already tried prodrg2 but no success. pls suggest a way for making .itp file .. residue already defined in ffgmx.rtp. ...already read earlier query posted but could not find an ans. _ Get the new Windows Live Messenger! http://get.live.com/messenger/overview___ 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 are you
Hi, Dr. Liang Please use PRODRG server. http://davapc1.bioch.dundee.ac.uk/programs/prodrg/ or you can write some script to convert Material studio pdb file to PDB bank format. Thanks. On 10/31/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote: > > Sir: > How are you! I am a new user of gmx.At first,sincere tribute to you > and all > the gmx developers! > I want to perform a molecular dynamics simulation on the tobramycin > aqueous > soluton by gmx. On the simulation process,I encounter some problem and I > can't > treat with it by myself and I hope you will give me a hand. > Tobramycin is a aminoglycosidic substance, Its pdb file is not > availabe in the > PDB bank, so I generate it with a comercial software Material studio. but > it is > not in consistent with gmx command of pdb2gmx. I want to know how can I > deal with > it and it the other way to generate a pdb file of tobramycin in gmx > format. > At the same time, how to obtain the parameter of tobramycin in gmx > opls > format? > Thank you and I am looking forward to hearing from you soon! > > Best wishes > zhuliang > > > > > -- > Dr.Liang Zhu > Department of Chemical Engineering > School of Chemical Engineering and Technology > Tianjin University Tianjin, 300072 P. R. China > > Tel: +86-22-27405754 Fax:+86-22-27374971 > ___ > 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 > -- Sincerely yours, James Jianzhang ___ 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 are you
Sir: How are you! I am a new user of gmx.At first,sincere tribute to you and all the gmx developers! I want to perform a molecular dynamics simulation on the tobramycin aqueous soluton by gmx. On the simulation process,I encounter some problem and I can't treat with it by myself and I hope you will give me a hand. Tobramycin is a aminoglycosidic substance, Its pdb file is not availabe in the PDB bank, so I generate it with a comercial software Material studio. but it is not in consistent with gmx command of pdb2gmx. I want to know how can I deal with it and it the other way to generate a pdb file of tobramycin in gmx format. At the same time, how to obtain the parameter of tobramycin in gmx opls format? Thank you and I am looking forward to hearing from you soon! Best wishes zhuliang -- Dr.Liang Zhu Department of Chemical Engineering School of Chemical Engineering and Technology Tianjin University Tianjin, 300072 P. R. China Tel: +86-22-27405754 Fax:+86-22-27374971 ___ 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 compare the simulated structure of the same peptide to the NMR strucutre?
[EMAIL PROTECTED] wrote: Hi, all I have simulated a beta-hairpin folded in explicit water, I want to compare the simulated structure to the experimental structure using NMR. Can you tell me how to do it? Thanks a lot! fufengliu Look in GROMACS manual section 7.4 for clues on what the GROMACS utilities do. Then read the man pages of likely suspects. 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] How compare the simulated structure of the same peptide to the NMR strucutre?
Hi, all I have simulated a beta-hairpin folded in explicit water, I want to compare the simulated structure to the experimental structure using NMR. Can you tell me how to do it? Thanks a lot! fufengliu ___ 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] editconf -mead
marcos wrote: Hi, editconf -mead writes a .pqr with a format "%10.5f%10.5f%10.5f" while it should be "%8.3f%8.3f%8.3f". Also the charges and radius are written in "%8.4f%8.4f" while the program pdb2pqr writes as "%8.4f%7.4f" I changed line 167 of pdbio.c from: strcpy(pdbform,"%-6s%5u %-4.4s %3.3s %c%4d%10.5f%10.5f%10.5f%8.4f% 8.4f\n"); to strcpy(pdbform,"%-6s%5u %-4.4s %3.3s %c%4d%8.3%8.3f%8.3f%8.4f%7.4f \n"); and the .pqr is now ok. Will this change affect other programs? I'm not aware that there is a standard for the PQR format. It's a hacked derivative of a PDB file. Some software that claims to read them probably constrains the format as for a PDB file, but others expect a free-form white-space-delimited format (e.g APBS, for which pdb2pqr prepares input). The two are not mutually consistent, so there will be problems. It's straightforward to write a Perl script to convert from the above formats you describe in order to make some PQR-reading software happy. If someone writes one, add it to the contributions section of the GROMACS webpage. 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] bug energy - continuity md
Ricardo Gobato wrote: In middle on molecular danimics have one bug power energy, have one exit the file traj.trr For continuity md with file traj.trr, write the comand 1. Don't claim a bug unless you actually have one - i.e. have at least a reproducible test case, and preferably code patch to fix it. Claiming bugs annoys the people who've worked hard on the software, who mostly read this list, and are very good about actively supporting their software. Annoying them is counter-productive for you. 2. Use a spell-checker... if you want people to spend their valuable time helping you, then you should make it easy for them to help you, by writing in at least correctly-spelled English. Then, proof-read before you send the email. I appreciate that English probably isn't your first language, but your first "sentence" isn't even close. 3. Try to find your own answers by reading documentation. You'll learn to be better at avoiding problems that way. Both the GROMACS manual and wiki tell you the information you're looking for. 4. Even if they wanted to help you, nobody can tell you the command you need to use, since it depends on a whole host of things you've not told us. :-) What you can do is read this page http://wiki.gromacs.org/index.php/Doing_Restarts and work it out for yourself. 5. "Please" is a good word to use when you're asking for free help. :-) Regards, 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] bug energy - continuity md
In middle on molecular danimics have one bug power energy, have one exit the file traj.trr For continuity md with file traj.trr, write the comand .. _ Conheça o Windows Live Spaces, a rede de relacionamentos conectada ao Messenger! http://spaces.live.com/signup.aspx___ 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] quasiharmonic eigenvalue units / Schlitter entropy
Dear Marcin, You can contact me off list for a script that calculates the QH entropies from the output of g_covar. Also, IIRC there should be a version of g_covar that already does it somewhere (CVS-?). Ran. On Wed, 31 Oct 2007 17:40:45 + Marcin Krol <[EMAIL PROTECTED]> wrote: Dear All, Sorry for the repeated question, but I'm a bit lost when I want to get frequencies of modes from quasiharmonic analysis done with g_covar. From what I understood in QH omega = sqrt(kT/lambda), where omega is the radial frequency, k - Boltzmann const, T-temp, and lambda is the eigenvalue. In order to get the units right lambda needs to be in length^2*mass units. Is it nm^2*amu? I need the frequencies to calculate entropy estimate from QH analysis. However, another way of getting the entropy estimate would be to get it from Schlitter formula. Then, I wouldn't need to diagonalize the covariance matrix. Is there a way to request the calculation of Schlitter entropy after the covariance matrix is calculated, but before g_covar starts diagonalization? Thanks in advance marcin -- Dr Marcin Krol Biomolecular Modelling Laboratory Cancer Research UK e-mail: [EMAIL PROTECTED] AND Department of Bioinformatics Collegium Medicum Jagiellonian University e-mail: [EMAIL PROTECTED] ___ 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 -- Ran Friedman Postdoctoral Fellow Computational Structural Biology Group (A. Caflisch) Institute of Biochemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich, Switzerland Tel. +41-44-6354493 Skype: ran.friedman -- ___ 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] editconf -mead
3.3.1 and 3.3.2 IIRC in 3.1.4 it was ok Marcos On Wed, 2007-10-31 at 18:34 +0100, Ran Friedman wrote: > Dear Marco, > > Which version? > > Ran. > > marcos wrote: > > Hi, > > > > editconf -mead writes a .pqr with a format "%10.5f%10.5f%10.5f" while it > > should be "%8.3f%8.3f%8.3f". > > Also the charges and radius are written in "%8.4f%8.4f" while the > > program pdb2pqr writes as "%8.4f%7.4f" > > > > I changed line 167 of pdbio.c from: > > strcpy(pdbform,"%-6s%5u %-4.4s %3.3s %c%4d%10.5f%10.5f%10.5f%8.4f% > > 8.4f\n"); > > > > to > > > > strcpy(pdbform,"%-6s%5u %-4.4s %3.3s %c%4d%8.3%8.3f%8.3f%8.4f%7.4f > > \n"); > > > > and the .pqr is now ok. Will this change affect other programs? > > > > Thanks, > > > > Marcos Villarreal > > > > > > ___ > 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] quasiharmonic eigenvalue units / Schlitter entropy
Dear All, Sorry for the repeated question, but I'm a bit lost when I want to get frequencies of modes from quasiharmonic analysis done with g_covar. From what I understood in QH omega = sqrt(kT/lambda), where omega is the radial frequency, k - Boltzmann const, T-temp, and lambda is the eigenvalue. In order to get the units right lambda needs to be in length^2*mass units. Is it nm^2*amu? I need the frequencies to calculate entropy estimate from QH analysis. However, another way of getting the entropy estimate would be to get it from Schlitter formula. Then, I wouldn't need to diagonalize the covariance matrix. Is there a way to request the calculation of Schlitter entropy after the covariance matrix is calculated, but before g_covar starts diagonalization? Thanks in advance marcin -- Dr Marcin Krol Biomolecular Modelling Laboratory Cancer Research UK e-mail: [EMAIL PROTECTED] AND Department of Bioinformatics Collegium Medicum Jagiellonian University e-mail: [EMAIL PROTECTED] ___ 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] editconf -mead
Dear Marco, Which version? Ran. marcos wrote: > Hi, > > editconf -mead writes a .pqr with a format "%10.5f%10.5f%10.5f" while it > should be "%8.3f%8.3f%8.3f". > Also the charges and radius are written in "%8.4f%8.4f" while the > program pdb2pqr writes as "%8.4f%7.4f" > > I changed line 167 of pdbio.c from: > strcpy(pdbform,"%-6s%5u %-4.4s %3.3s %c%4d%10.5f%10.5f%10.5f%8.4f% > 8.4f\n"); > > to > > strcpy(pdbform,"%-6s%5u %-4.4s %3.3s %c%4d%8.3%8.3f%8.3f%8.4f%7.4f > \n"); > > and the .pqr is now ok. Will this change affect other programs? > > Thanks, > > Marcos Villarreal > > ___ 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] editconf -mead
Hi, editconf -mead writes a .pqr with a format "%10.5f%10.5f%10.5f" while it should be "%8.3f%8.3f%8.3f". Also the charges and radius are written in "%8.4f%8.4f" while the program pdb2pqr writes as "%8.4f%7.4f" I changed line 167 of pdbio.c from: strcpy(pdbform,"%-6s%5u %-4.4s %3.3s %c%4d%10.5f%10.5f%10.5f%8.4f% 8.4f\n"); to strcpy(pdbform,"%-6s%5u %-4.4s %3.3s %c%4d%8.3%8.3f%8.3f%8.4f%7.4f \n"); and the .pqr is now ok. Will this change affect other programs? Thanks, Marcos Villarreal ___ 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] Gromacs on IBM cluster
I have aprox. 81000 atoms. The system worked on a Itanium 2 cluster. On the IBM machine I've used the IBM compilers. I'm going to give it a try with gcc. Thank you Marius Retegan On 10/31/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > Marius Retegan wrote: > > 32 Gb on each node of the cluster. > > Maybe I should add that I've also ran CPMD and cp2k jobs on the > > cluster but I've never had memory problems. > > Marius Retegan > It could still be too little, since this is the additional memory. What > kind of system are you using, how many atoms? Does a small water box > work? There have been problems with compilation on IBM machines as well, > in particular when using IBM compilers. Recompiling with gcc resolves that. > > > > > On 10/30/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > >> Marius Retegan wrote: > >>> Dear Gromacs users > >>> > >>> I'm having some troubles running grompp on a IBM cluster P575 with AIX > >>> 5.3 installed. > >>> This is the error message that I'm getting: > >>> > >>> processing coordinates... > >>> double-checking input for internal consistency... > >>> renumbering atomtypes... > >>> --- > >>> Program grompp_d, VERSION 3.3.1 > >>> Source code file: smalloc.c, line: 113 > >>> > >>> Fatal error: > >>> calloc for nbsnew (nelem=677329, elsize=148, file grompp.c, line 723) > >> This says it wants one Gb of RAM. How much do you have? > >> You can run grompp on a machine with a lot of memory and the mdrun on > >> your cluster. > >>> --- > >>> > >>> "I'm An Oakman" (Pulp Fiction) > >>> : Not enough space > >>> > >>> While digging into the archive I've managed to find this post > >>> http://www.gromacs.org/pipermail/gmx-users/2006-February/020066.html, > >>> which basically says that there is not enough memory for the job. My > >>> job is lunched with LoadLeveler where I can define the @resources = > >>> ConsumableMemory (value), but if this is not defined in the > >>> LoadLeveler script, I think that the program should thake as much > >>> memory as it requires. > >>> So my question is why does Gromacs, a program renowned for low memory > >>> requirements, give this error message? > >>> > >>> Thank you > >>> Marius Retegan > >>> ___ > >>> 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 > >> > > ___ > > 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
Re: [gmx-users] g_rmsf Segmentation fault
Tommy Carstensen wrote: To the gmx-users, When executing: g_rmsf -f traj.trr -s topol.tpr -o rmsf.xvg -aniso I get the following error after running through all the frames: Segmentations fault If I don't include the aniso flag I don't get an segfault. Can anyone explain to me, why it is not working with the aniso flag? probably a bug. maybe it works if you input a pdbfile with reference B values. Anyway you're welcome to submit a bugzilla, please upload input files to reproduce the problem. Kind regards, Tommy Tommy Carstensen UCD School of Biomolecular and Biomedical Sciences Conway Institute University College Dublin Dublin 4, Ireland http://enzyme.ucd.ie/group_members/tommy ___ 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
[gmx-users] g_rmsf Segmentation fault
To the gmx-users, When executing: g_rmsf -f traj.trr -s topol.tpr -o rmsf.xvg -aniso I get the following error after running through all the frames: Segmentations fault If I don't include the aniso flag I don't get an segfault. Can anyone explain to me, why it is not working with the aniso flag? Kind regards, Tommy Tommy Carstensen UCD School of Biomolecular and Biomedical Sciences Conway Institute University College Dublin Dublin 4, Ireland http://enzyme.ucd.ie/group_members/tommy ___ 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_sas problem
tangxuan wrote: Hi Mark, Thanks very much for your reply. I checked the structure of A and B at these three ps, and there is no much change in the structures. Then I calculated the reside area in A+B at these three specific time (1536,15937,15938), and it shows that there are a big diffrence in size of area at many resides between three ps. Maybe the big changes of total SAS in interaction region at 15938 ps is because of big size of two subunits(each has 471 resides). What is your idea? Tang, this is most likely all due to periodic boundary conditions. Please run trjconv -pbc mol -ur compact on your trajectory. Thanks, Tang jiaowei On Wed, 2007-10-31 at 01:59 +1100, Mark Abraham wrote: tangxuan wrote: Yes, the default value of -pbc is 'yes'. I did not add it in my command, but i think pbc should has been considered. It seems there is no contact between the two subunits, but at some specific time the total ASA of interaction region is very high(shown below). time total SAS of interaction region 15936 1.160997 15937 1.091004 15938 86.954 Have a look at your trajectory to see what the structures are doing here. 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 -- 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] g_sas problem
Hi Mark, Thanks very much for your reply. I checked the structure of A and B at these three ps, and there is no much change in the structures. Then I calculated the reside area in A+B at these three specific time (1536,15937,15938), and it shows that there are a big diffrence in size of area at many resides between three ps. Maybe the big changes of total SAS in interaction region at 15938 ps is because of big size of two subunits(each has 471 resides). What is your idea? Thanks, Tang jiaowei On Wed, 2007-10-31 at 01:59 +1100, Mark Abraham wrote: > tangxuan wrote: > > Yes, the default value of -pbc is 'yes'. I did not add it in my command, > > but i think pbc should has been considered. It seems there is no > > contact between the two subunits, but at some specific time the total > > ASA of interaction region is very high(shown below). > > > > time total SAS of interaction region > > 15936 1.160997 > > 15937 1.091004 > > 15938 86.954 > > Have a look at your trajectory to see what the structures are doing here. > > 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] Gromacs on IBM cluster
Marius Retegan wrote: 32 Gb on each node of the cluster. Maybe I should add that I've also ran CPMD and cp2k jobs on the cluster but I've never had memory problems. Marius Retegan It could still be too little, since this is the additional memory. What kind of system are you using, how many atoms? Does a small water box work? There have been problems with compilation on IBM machines as well, in particular when using IBM compilers. Recompiling with gcc resolves that. On 10/30/07, David van der Spoel <[EMAIL PROTECTED]> wrote: Marius Retegan wrote: Dear Gromacs users I'm having some troubles running grompp on a IBM cluster P575 with AIX 5.3 installed. This is the error message that I'm getting: processing coordinates... double-checking input for internal consistency... renumbering atomtypes... --- Program grompp_d, VERSION 3.3.1 Source code file: smalloc.c, line: 113 Fatal error: calloc for nbsnew (nelem=677329, elsize=148, file grompp.c, line 723) This says it wants one Gb of RAM. How much do you have? You can run grompp on a machine with a lot of memory and the mdrun on your cluster. --- "I'm An Oakman" (Pulp Fiction) : Not enough space While digging into the archive I've managed to find this post http://www.gromacs.org/pipermail/gmx-users/2006-February/020066.html, which basically says that there is not enough memory for the job. My job is lunched with LoadLeveler where I can define the @resources = ConsumableMemory (value), but if this is not defined in the LoadLeveler script, I think that the program should thake as much memory as it requires. So my question is why does Gromacs, a program renowned for low memory requirements, give this error message? Thank you Marius Retegan ___ 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 ___ 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] grompp error for alamethicin
pragya chohan wrote: hi ... when i run grompp i get an error " No such moleculetype Protein " ... i included itp for ACE and AIB after generating them from PRODRG2 server... my top file is : Check out http://wiki.gromacs.org/index.php/Errors#Fatal_error:_No_such_moleculetype_XXX 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] grompp error for alamethicin
hi ... when i run grompp i get an error " No such moleculetype Protein " ... i included itp for ACE and AIB after generating them from PRODRG2 server... my top file is : ; Include forcefield parameters #include "ffG43a1.itp" ; Include chain topologies #include "ace.itp" #include "aib.itp" ; Include water topology #include "spce.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include generic topology for ions #include "ions.itp" [ system ] ; Name Protein in water [ molecules ] ; Compound#mols Protein 1 The command i m using is : grompp -f 7eq_w.mdp -c ala.gro -p aquapo_grom.top -o alam.tpr ala.gro is generated using editconf. The .mdp file is integrator = md define = -DPOSRES -DFLEX_SPC dt = 0.002 nsteps = 25000 nstxout = 500 ns_type = grid pbc = xyz constraints = hbonds constraints_algorithm= shake coulombtype = PME vdwtype = cut-off rcoloumb = 1.4 Tcoupl = berendsen pcoupl = berendsen tau_t= 0.1 0.1 tc_grps = POPC SOL ref_t= 300 300 ref_p= 1.0 pcoupltype = isotropic compressibility = 4.5e-5 gen_temp = 300 Pls reply as soon as possible _ Get the new Windows Live Messenger! http://get.live.com/messenger/overview___ 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] Gromacs on IBM cluster
32 Gb on each node of the cluster. Maybe I should add that I've also ran CPMD and cp2k jobs on the cluster but I've never had memory problems. Marius Retegan On 10/30/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > Marius Retegan wrote: > > Dear Gromacs users > > > > I'm having some troubles running grompp on a IBM cluster P575 with AIX > > 5.3 installed. > > This is the error message that I'm getting: > > > > processing coordinates... > > double-checking input for internal consistency... > > renumbering atomtypes... > > --- > > Program grompp_d, VERSION 3.3.1 > > Source code file: smalloc.c, line: 113 > > > > Fatal error: > > calloc for nbsnew (nelem=677329, elsize=148, file grompp.c, line 723) > This says it wants one Gb of RAM. How much do you have? > You can run grompp on a machine with a lot of memory and the mdrun on > your cluster. > > --- > > > > "I'm An Oakman" (Pulp Fiction) > > : Not enough space > > > > While digging into the archive I've managed to find this post > > http://www.gromacs.org/pipermail/gmx-users/2006-February/020066.html, > > which basically says that there is not enough memory for the job. My > > job is lunched with LoadLeveler where I can define the @resources = > > ConsumableMemory (value), but if this is not defined in the > > LoadLeveler script, I think that the program should thake as much > > memory as it requires. > > So my question is why does Gromacs, a program renowned for low memory > > requirements, give this error message? > > > > Thank you > > Marius Retegan > > ___ > > 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 > ___ 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] No improvement in scaling on introducing flow control
himanshu khandelia wrote: > Hi Carsten, > > The benchmarks were made is 1 NIC/node, and yet the scaling is bad. > Does that mean that there is indeed network congestion ? We will try > using back to back connections soon, Hi Himanshu, In my opinion the most probable scenario is that the bandwidth of the single gigabit connection is not sufficient for the four very fast CPUs you have on each node. I would do an 8 CPU benchmark with a back-to-back connection as here the chance for network congestion is minimized. If the benchmarks stay as they were with the switch (they might be a bit better because you do not have the switch's latency), I would try to make use of both interfaces to double the bandwidth. This can easily be done with OpenMPI. You could also do a 16 CPU benchmark on 16 nodes so that the processes do not need to share the network interface. If the scaling is better compared to 16 CPUs on 4 nodes, it is an indication for the bandwidth problem. Carsten > > -himanshu > > > > maybe your problem is not even flow control, but the limited network > bandwidth which is shared among 4 CPUs in your case. I also have done > benchmarks on Woodcrests >> (2.33 GHz) and was not able to scale an 8 atom system beyond 1 node with >> Gbit Ethernet. Looking in more detail, the time gained by the additional 4 >> CPUs of a >> second node was exactly balanced by the extra communication. I used only 1 >> network interface for that benchmark, leaving effectively only 1/4 th of the >> bandwidth >> for each CPU. Using two interfaces with OpenMPI did not double the network >> performance on our cluster. In my tests nodes with 2 CPUs sharing one NIC >> were faster >> than nodes with 4 CPUs sharing two NICs. Could be on-node contention, since >> both interfaces probably end up on the same bus internally. >> >> Are the benchmarks made with 1 or 2 NICs/node? If they are for 1 NIC/node >> then there should be no network congestion for the case of 8 CPUs (=2 >> nodes). You could >> try a back-to-back connection between two nodes to be absolutely shure that >> the rest of the network (switch etc.) does not play a role. I would try that >> and repeat >> the benchmark for 8 CPUs. See if you get a different value. >> ## > ___ > 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] langevin dynamics
From: "Syma Khalid" <[EMAIL PROTECTED]> Reply-To: [EMAIL PROTECTED],Discussion list for GROMACS users To: "'Discussion list for GROMACS users'" Subject: [gmx-users] langevin dynamics Date: Tue, 30 Oct 2007 16:55:59 - Dear all, I was wondering if someone could offer some advice? I would like to run an atomistic langevin dynamics simulation (as I don't want to include water explicitly). If I add the appropriate langevin dynamics options in the mdp file, then is there any reason why I shouldn't use explicit counter ions (unfortunately my protein has an overall charge)? Obviously I would use periodic boundary conditions so the ions don't wander off. This question has come up many times on the mailing list and I have answered in many times. I will answer it once again. Langevin dynamics is not a magic option that replaces your solvent. Langevin dynamics only influences the dynamics, not the distributions. If you choose a high friction, it might mimick the friction of water, but it does nothing to your potentials. Therefore you can not use Langevin dynamics will a normal protein force field and just leave out the water. This will produce a vacuum simulation. Berk. _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview ___ 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
