Re: [gmx-users] GROMACS vs NAMD
Dibyadeep Paul wrote: Hii... Could somebody kindly point out to me the essential difference between the simulation procedures between NAMD and GROMACS. I am familiar with NAMD, but since I am running it on a single processor machine I hear that GROMACS would be much more efficient. Is there any comparison of the results available on publicly available literature. If so it would be very kind if somebody knowledgeable could kindly point that out to me, or send me the relevent paper. On the GROMACS website there is a list of papers, one "neutral" paper did exactly this comparison, although it seems like they want to stay friends with everyone :). In the GROMACS 4 paper there is a comparison done by us with NAMD and Desmond figures from the literature. NAMD is roughly 4 times slower than GROMACS, predominantly because of single processor performance. However GROMACS 4 can also do constraints in parallel which means one can take larger time steps than with other packages, and this makes the gap even wider. Sincerely Dibyadeep ___ 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. 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] step.pdb files during EM
Dear list, I ran EM (energy minimisation) of TIP5P water model using gromacs/3.3.2 version. My output says : Steepest Descents converged to Fmax < 100 in 427 steps. Moreover, my output.gro file looks ok after the run. But in the directory, there were some files (8), called step.pdb, generated. But, it is said, actually simulation crashed, that is why these files are being generated ( Thread 2004 January). But in my case, if the program was crashed, then why it ran till 427th step to finish EM to the desired accuracy. Furthermore, when I inspected the output file, I found the following similar messages on 8 occasions : "t = 0.023 ps: Water molecule starting at atom 356 can not be settled. Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates". I constructed the water box using packmol program. If I want to avoid these error messages, What should I do? thanks in advance, Jestin ___ 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 vs NAMD
> Hii... > > Could somebody kindly point out to me the essential difference between the > simulation procedures between NAMD and GROMACS. Not really... the general procedure is the same, but the names for things change a bit. > I am familiar with NAMD, > but > since I am running it on a single processor machine I hear that GROMACS > would be much more efficient. Is there any comparison of the results > available on publicly available literature. If so it would be very kind if > somebody knowledgeable could kindly point that out to me, or send me the > relevent paper. I'm not aware that there is one. In general, doing meaningful and fair comparisons is difficult because the performance of all such codes is strongly dependent on system size, hardware attributes, which algorithms you want to use and how much effort has gone into optimizing them. Still, the general observation that GROMACS will be faster on a single-processor machine is true. You should try it yourself on your hardware and see. 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] incorporation of distance restraint into the topology file
> Hi all, > > I have a question regarding the creating a disulphide bridge. If I want to > impose a position restraint on this bond how can I incorporate it into the > topology file? It is explained in the manual but the explanation for the > last three columns is not clear. I could not decide to put what numbers > into these columns. > > P.S: I use Gromacs 3.3.1 See example late in section 4.3.4 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] GROMACS vs NAMD
Hii... Could somebody kindly point out to me the essential difference between the simulation procedures between NAMD and GROMACS. I am familiar with NAMD, but since I am running it on a single processor machine I hear that GROMACS would be much more efficient. Is there any comparison of the results available on publicly available literature. If so it would be very kind if somebody knowledgeable could kindly point that out to me, or send me the relevent paper. Sincerely Dibyadeep ___ 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] incorporation of distance restraint into the topology file
Hi all, I have a question regarding the creating a disulphide bridge. If I want to impose a position restraint on this bond how can I incorporate it into the topology file? It is explained in the manual but the explanation for the last three columns is not clear. I could not decide to put what numbers into these columns. P.S: I use Gromacs 3.3.1 Thanks in advance Ozge Engin = Computational Science & Engineering Koc University ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with mpi configuration.
Since you didn't show us the problems you met.. try following this: #1) Download essential packages #1.1) mpich wget http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/mpich2-1.0.6p1.tar.gz #1.2) fftw wget ftp://ftp.fftw.org/pub/fftw/fftw-3.1.2.tar.gz #1.3) gromacs wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-3.3.2.tar.gz #2) compile packages: #2.1) mpich tar xvfz mpich2-1.0.6p1.tar.gz cd mpich2-1.0.6p1 make distclean ./configure --with-device=ch3:nemesis --enable-fast --disable-cxx --enable-error-checking=no CFLAGS=-O3 FFLAGS=-O3 make make install make distclean cd .. #2.2) fftw single tar xvfz fftw-3.1.2.tar.gz cd fftw-3.1.2 make distclean ./configure --enable-float --enable-sse --enable-threads make make install make distclean cd .. #2.3) gromacs single tar xvfz gromacs-3.3.2.tar.gz cd gromacs-3.3.2 ./configure --enable-mpi --program-suffix=_mpi --prefix=/usr/local/gromacs332 make make install make links make distclean cd .. #2.4) fftw double cd fftw-3.1.2 ./configure --enable-sse2 --enable-threads make make install make distclean cd .. #2.2) gromacs double cd gromacs-3.3.2 ./configure --enable-mpi --program-suffix=_mpi_d --prefix=/usr/local/gromacs332 --enable-double make make install make links make distclean cd .. On Mon, Mar 3, 2008 at 3:09 PM, mario ciappy <[EMAIL PROTECTED]> wrote: > Dear all, > I'm tried to configure gromacs in parallel but I have meet some problems. > I don't understand if the problems are relative to mpi or gromacs > configuration. For this reason I'd be grateful if you explained a detailed > installation procedure of all that require to run gromacs in parallel, > started by mpi/lam configuration. I now that is an hard and demanding > request, but it is a big help for me because you are only resource. > > Thank's in advance > > Mario > > > > > > L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail > ___ > 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 > -- Diego Enry B. Gomes Laboratório de Modelagem e Dinamica Molecular Universidade Federal do Rio de Janeiro - Brasil. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] problem with mpi configuration.
Dear all, I'm tried to configure gromacs in parallel but I have meet some problems. I don't understand if the problems are relative to mpi or gromacs configuration. For this reason I'd be grateful if you explained a detailed installation procedure of all that require to run gromacs in parallel, started by mpi/lam configuration. I now that is an hard and demanding request, but it is a big help for me because you are only resource. Thank's in advance Mario - - L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail___ 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] Electrostatic forces
Thanks for your reply Mark. George -Original Message- From: [EMAIL PROTECTED] on behalf of Mark Abraham Sent: Mon 3/3/2008 1:24 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Electrostatic forces > Hello > > I am trying to extract the electrostatic part of the forces in a > trajectory. > The way I do it is by re-running the simulation and having "swiched-off" > the bonded and the LJ terms. Is this correct? Yeah, unless you've used restraints, disperson corrections or something else weird I can't think of now. Consider the contents of your .mdp file and whether the options you chose anything to the Hamiltonian - i.e. the energy evaluation - that you haven't already removed. 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] DPPC lipid model in Gromos 53a5
> Mark Abraham wrote: >>> Dear all, >>> >>> In the definition of the DPPC lipid molecule in ffG53a5.rtp I found, >>> that >>> some >>> dihedral angles are defined twice: >>> >>> [ dihedrals ] >>> ; aiajakal gromos type >>>C33 N C32 C31 gd_29 >>> N C32 C31 O32 gd_4 >>> N C32 C31 O32 gd_36 <- >>>C32 C31 O32 P gd_29 >>>C31 O32 P O31 gd_20 >>>C31 O32 P O31 gd_27 <- >>>O32 P O31C3 gd_20 >>>O32 P O31C3 gd_27 <- >>> >>> Is this a mistake or on purpose ? >>> >>> Does the second entry overwrite the first entry, i.e. the values of the >>> second >>> entry are used ? >> >> It depends on the functional form - you'll need to look up these gd_?? >> macros in the forcefield .itp file. A second function with the same >> function type will over-write the first. I think it does so silently. A >> different function type on the same atoms is accepted silently. >> > > I'm not sure this is correct: check your top file. If you have two > dihedrals in the top file both are evaluated and the effective > interaction is the sum of these. This is a way to fake a more > complicated dihedral term. Ah, yes, David is right (as usual). I tested this, and found that a gmxdump of a grompp of a topology that included a second bonded interaction of the same type on the same atoms reveals that both functions are used. Please accept my apologies for the mistake - I believe I extrapolated incorrectly from the fact that multiple [ dihedraltypes ] entries with the same atom types and function type do not add. In the original example (and my test case) the functions are explicitly defined, and thus the [ dihedraltypes ] lookup is not used. To return to the issue in the original post - one could well wish to have periodic dihedrals with different periodicities to add to give a more complex functional form than is possible with a single periodic dihedral. More perverse applications could be imagined :-) 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] DPPC lipid model in Gromos 53a5
The gd_?? macros are #define gd_4180.000 5.86 1 ; N-CHn-CHn-OA (lipid) 1.4 #define gd_36 0.000 8.62 3 ; N-CHn-CHn-OA (lipid) 2.1 #define gd_20 0.000 5.09 2 ; O-P-O- (dna, lipids) 1.2 #define gd_27 0.000 3.19 3 ; O-P-O- (dna, lipids) 0.8 The two repeating dihedral definitions are certainly in the .top file, because I have copied the DPPC definition from ffG53a5.rtp into an .itp file as a starting point for developing a 'good' DPPC model consistent with the Gromos 53a5 force field. Many thanks for your comments Andreas David van der Spoel wrote: Mark Abraham wrote: Dear all, In the definition of the DPPC lipid molecule in ffG53a5.rtp I found, that some dihedral angles are defined twice: [ dihedrals ] ; aiajakal gromos type C33 N C32 C31 gd_29 N C32 C31 O32 gd_4 N C32 C31 O32 gd_36 <- C32 C31 O32 P gd_29 C31 O32 P O31 gd_20 C31 O32 P O31 gd_27 <- O32 P O31C3 gd_20 O32 P O31C3 gd_27 <- Is this a mistake or on purpose ? Does the second entry overwrite the first entry, i.e. the values of the second entry are used ? It depends on the functional form - you'll need to look up these gd_?? macros in the forcefield .itp file. A second function with the same function type will over-write the first. I think it does so silently. A different function type on the same atoms is accepted silently. I'm not sure this is correct: check your top file. If you have two dihedrals in the top file both are evaluated and the effective interaction is the sum of these. This is a way to fake a more complicated dihedral term. 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 force field discussion
Hi Patrick, we recently parametrized DOPC in the generalized Amber FF (GAFF). The Gromacs input files (itp & top, mdp) as well as a pdb file are available on our website. Best, Rainer On Mar 3, 2008, at 11:57 AM, patrick fuchs wrote: Hi David, since updated GROMOS force fields are now available within GROMACS, I agree one does not need to use ffgmx, at least for standard simulations. The only problem is for lipid/protein simulations. The only publicly available I know that runs under GROMACS is the combination of Berger lipids with ffgmx (on the website of Peter Tieleman). For someone starting a project of lipid/protein simulations, there is a priori no other public alternative (using GROMACS), although I know some new parameters are about to be published. Cheers, Patrick David van der Spoel a écrit : Reay, Andrew wrote: Hi, I am trying to find out why the Gromacs force field is no longer recommended for use. I've searched the mailing list archives for quite awhile to find the discussion but have been unsuccessful. Can anybody tell me where to find that discussion? Thanks very much. The never has bee a GROMACS force field, although we named it such to avoid confusion with official "GROMOS" force fields. What used to be called the GROMACS force field was basically GROMOS87 + changes due to Van Buuren & Berendsen (J.Phys.Chem. 97 [1993] 9206) plus changes on aromatic groups from an unpublished paper from the Van Gusteren group (these parameters are given in my paper in J.Biomol. NMR 8 (1996) p.229). This is described in the manual. In other words there is no good description of ths force field in a single paper. For good reasons the Van Gunsteren group have updated their GROMOS force field on a number of occasions, and these force field are now supported in GROMACS, along with a few others. Although it is still possible to use the old parameter set, please do not call it "The GROMACS force field", but use the description above. Most referees fro scientific papers will (should) raise their eyebrows when reading that this parameter set was used, so this is another reason to shy away from it. Andy ___ 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 -- _ new E-mail address: [EMAIL PROTECTED] Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ 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 __ Dr. Rainer Böckmann Theoretical & Computational Membrane Biology Center for Bioinformatics Saar Universität des Saarlandes Gebäude C7.1, EG D-66041 Saarbrücken, Germany Phone: ++49 +681 302-64169 / 68627 FAX: ++49 +681 302-64180 E-Mail: [EMAIL PROTECTED] http://www.bioinf.uni-sb.de/RB/ ___ ___ 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] Electrostatic forces
> Hello > > I am trying to extract the electrostatic part of the forces in a > trajectory. > The way I do it is by re-running the simulation and having "swiched-off" > the bonded and the LJ terms. Is this correct? Yeah, unless you've used restraints, disperson corrections or something else weird I can't think of now. Consider the contents of your .mdp file and whether the options you chose anything to the Hamiltonian - i.e. the energy evaluation - that you haven't already removed. 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] DPPC lipid model in Gromos 53a5
Mark Abraham wrote: Dear all, In the definition of the DPPC lipid molecule in ffG53a5.rtp I found, that some dihedral angles are defined twice: [ dihedrals ] ; aiajakal gromos type C33 N C32 C31 gd_29 N C32 C31 O32 gd_4 N C32 C31 O32 gd_36 <- C32 C31 O32 P gd_29 C31 O32 P O31 gd_20 C31 O32 P O31 gd_27 <- O32 P O31C3 gd_20 O32 P O31C3 gd_27 <- Is this a mistake or on purpose ? Does the second entry overwrite the first entry, i.e. the values of the second entry are used ? It depends on the functional form - you'll need to look up these gd_?? macros in the forcefield .itp file. A second function with the same function type will over-write the first. I think it does so silently. A different function type on the same atoms is accepted silently. I'm not sure this is correct: check your top file. If you have two dihedrals in the top file both are evaluated and the effective interaction is the sum of these. This is a way to fake a more complicated dihedral term. 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 -- David van der Spoel, Ph.D. 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] DPPC lipid model in Gromos 53a5
> Dear all, > > In the definition of the DPPC lipid molecule in ffG53a5.rtp I found, that > some > dihedral angles are defined twice: > > [ dihedrals ] > ; aiajakal gromos type >C33 N C32 C31 gd_29 > N C32 C31 O32 gd_4 > N C32 C31 O32 gd_36 <- >C32 C31 O32 P gd_29 >C31 O32 P O31 gd_20 >C31 O32 P O31 gd_27 <- >O32 P O31C3 gd_20 >O32 P O31C3 gd_27 <- > > Is this a mistake or on purpose ? > > Does the second entry overwrite the first entry, i.e. the values of the > second > entry are used ? Oh, and obviously the primary point of reference would be the paper where this forcefield was published... 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] DPPC lipid model in Gromos 53a5
> Dear all, > > In the definition of the DPPC lipid molecule in ffG53a5.rtp I found, that > some > dihedral angles are defined twice: > > [ dihedrals ] > ; aiajakal gromos type >C33 N C32 C31 gd_29 > N C32 C31 O32 gd_4 > N C32 C31 O32 gd_36 <- >C32 C31 O32 P gd_29 >C31 O32 P O31 gd_20 >C31 O32 P O31 gd_27 <- >O32 P O31C3 gd_20 >O32 P O31C3 gd_27 <- > > Is this a mistake or on purpose ? > > Does the second entry overwrite the first entry, i.e. the values of the > second > entry are used ? It depends on the functional form - you'll need to look up these gd_?? macros in the forcefield .itp file. A second function with the same function type will over-write the first. I think it does so silently. A different function type on the same atoms is accepted silently. 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] DPPC lipid model in Gromos 53a5
Dear all, In the definition of the DPPC lipid molecule in ffG53a5.rtp I found, that some dihedral angles are defined twice: [ dihedrals ] ; aiajakal gromos type C33 N C32 C31 gd_29 N C32 C31 O32 gd_4 N C32 C31 O32 gd_36 <- C32 C31 O32 P gd_29 C31 O32 P O31 gd_20 C31 O32 P O31 gd_27 <- O32 P O31C3 gd_20 O32 P O31C3 gd_27 <- Is this a mistake or on purpose ? Does the second entry overwrite the first entry, i.e. the values of the second entry are used ? Many thanks Andreas ___ 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] Electrostatic forces
Hello I am trying to extract the electrostatic part of the forces in a trajectory. The way I do it is by re-running the simulation and having "swiched-off" the bonded and the LJ terms. Is this correct? Thanks George ___ 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 force field discussion
David van der Spoel wrote: > patrick fuchs wrote: >> Hi David, >> since updated GROMOS force fields are now available within GROMACS, I >> agree one does not need to use ffgmx, at least for standard simulations. >> The only problem is for lipid/protein simulations. The only publicly >> available I know that runs under GROMACS is the combination of Berger >> lipids with ffgmx (on the website of Peter Tieleman). For someone >> starting a project of lipid/protein simulations, there is a priori no >> other public alternative (using GROMACS), although I know some new >> parameters are about to be published. >> Cheers, > > But the Berger et al force field is based upon OPLS, and hence it can > be combined with OPLS all atom FF. > These parameters were developed with united-atom OPLS. Tieleman and co-workers introduced modifications to allow the usage of these parameters with all atom OPLS (Tieleman et al., J. Phys. Condens. Matter 18 S1221-34, 2006). I would use it with cautious though, the results show significant differences between ffgmx and OPLSAA (Table 1 of the paper above). In addition, there can be an error in the range of 10 kCal/mol in the calculated cyclohexane to water transfer energies with OPLS (in any combination, Table 3 of Tieleman et al.). I found this alarming, but haven't seen results from other FFs - the error may be just as big. Ran. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with trjconv
> Hi all, > I am trying to use *trjconv command for -pbc but POPC molecules are > breaking > when visualize in VMD. The commands used are > grompp -f pr.mdp -c em_out.gro -p .top -n index.ndx -o out.tpr > trjconv -f em_out.gro -s out.tpr -o trj_out.gro -pbc inbox or cluster > or > whole > Thi trj_out.gro contain broken POPC molecules GROMACS doesn't ever write molecules that are broken across periodic boundaries. Thus either you've introduced a visual artefact with your use of VMD, or your EM produced a broken molecule through using a broken physical model. You should examine the nature of "broken", and/or try using ngmx to confirm what is really going on. Your grompp-trjconv sequence is not necessary for massaging the PBC behaviour of your EM output. trjconv will accept a .gro file for the -s flag, which you will see is indicated in the section of the output of "trjconv -h" that deals with the -s flag. This is quite general GROMACS behaviour. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with trjconv
Quoting sudheer babu <[EMAIL PROTECTED]>: > Hi all, > I am trying to use *trjconv command for -pbc but POPC molecules are breaking > when visualize in VMD. The commands used are > grompp -f pr.mdp -c em_out.gro -p .top -n index.ndx -o out.tpr > trjconv -f em_out.gro -s out.tpr -o trj_out.gro -pbc inbox or cluster or > whole Your scheme will not work because the structure in the .tpr file is the same as in your em_out.gro, which you claim to be broken. I'm assuming em_out.gro refers to your structure following energy-minimization? And if so, I'm wondering what you've done that's left a broken molecule following EM. Is your em_out.gro whole? -Justin > Thi trj_out.gro contain broken POPC molecules > Pls suggest me what options I have to use for -pbc? or any addition option I > have to use? > Thanks in advance... > Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (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] problem with trjconv
Hi all, I am trying to use *trjconv command for -pbc but POPC molecules are breaking when visualize in VMD. The commands used are grompp -f pr.mdp -c em_out.gro -p .top -n index.ndx -o out.tpr trjconv -f em_out.gro -s out.tpr -o trj_out.gro -pbc inbox or cluster or whole Thi trj_out.gro contain broken POPC molecules Pls suggest me what options I have to use for -pbc? or any addition option I have to use? 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
Re: [gmx-users] Gromacs force field discussion
patrick fuchs wrote: Hi David, since updated GROMOS force fields are now available within GROMACS, I agree one does not need to use ffgmx, at least for standard simulations. The only problem is for lipid/protein simulations. The only publicly available I know that runs under GROMACS is the combination of Berger lipids with ffgmx (on the website of Peter Tieleman). For someone starting a project of lipid/protein simulations, there is a priori no other public alternative (using GROMACS), although I know some new parameters are about to be published. Cheers, But the Berger et al force field is based upon OPLS, and hence it can be combined with OPLS all atom FF. Patrick David van der Spoel a écrit : Reay, Andrew wrote: Hi, I am trying to find out why the Gromacs force field is no longer recommended for use. I've searched the mailing list archives for quite awhile to find the discussion but have been unsuccessful. Can anybody tell me where to find that discussion? Thanks very much. The never has bee a GROMACS force field, although we named it such to avoid confusion with official "GROMOS" force fields. What used to be called the GROMACS force field was basically GROMOS87 + changes due to Van Buuren & Berendsen (J.Phys.Chem. 97 [1993] 9206) plus changes on aromatic groups from an unpublished paper from the Van Gusteren group (these parameters are given in my paper in J.Biomol. NMR 8 (1996) p.229). This is described in the manual. In other words there is no good description of ths force field in a single paper. For good reasons the Van Gunsteren group have updated their GROMOS force field on a number of occasions, and these force field are now supported in GROMACS, along with a few others. Although it is still possible to use the old parameter set, please do not call it "The GROMACS force field", but use the description above. Most referees fro scientific papers will (should) raise their eyebrows when reading that this parameter set was used, so this is another reason to shy away from it. Andy ___ 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. 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] Gromacs force field discussion
Hi David, since updated GROMOS force fields are now available within GROMACS, I agree one does not need to use ffgmx, at least for standard simulations. The only problem is for lipid/protein simulations. The only publicly available I know that runs under GROMACS is the combination of Berger lipids with ffgmx (on the website of Peter Tieleman). For someone starting a project of lipid/protein simulations, there is a priori no other public alternative (using GROMACS), although I know some new parameters are about to be published. Cheers, Patrick David van der Spoel a écrit : Reay, Andrew wrote: Hi, I am trying to find out why the Gromacs force field is no longer recommended for use. I've searched the mailing list archives for quite awhile to find the discussion but have been unsuccessful. Can anybody tell me where to find that discussion? Thanks very much. The never has bee a GROMACS force field, although we named it such to avoid confusion with official "GROMOS" force fields. What used to be called the GROMACS force field was basically GROMOS87 + changes due to Van Buuren & Berendsen (J.Phys.Chem. 97 [1993] 9206) plus changes on aromatic groups from an unpublished paper from the Van Gusteren group (these parameters are given in my paper in J.Biomol. NMR 8 (1996) p.229). This is described in the manual. In other words there is no good description of ths force field in a single paper. For good reasons the Van Gunsteren group have updated their GROMOS force field on a number of occasions, and these force field are now supported in GROMACS, along with a few others. Although it is still possible to use the old parameter set, please do not call it "The GROMACS force field", but use the description above. Most referees fro scientific papers will (should) raise their eyebrows when reading that this parameter set was used, so this is another reason to shy away from it. Andy ___ 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 -- _ new E-mail address: [EMAIL PROTECTED] Patrick FUCHS Equipe de Bioinformatique Genomique et Moleculaire INSERM U726, Universite Paris 7 Case Courrier 7113 2, place Jussieu, 75251 Paris Cedex 05, FRANCE Tel : +33 (0)1-44-27-77-16 - Fax : +33 (0)1-43-26-38-30 Web Site: http://www.ebgm.jussieu.fr/~fuchs ___ 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: Re: [gmx-users] procedure for creating an S-S bridge
So, from the explanation made within table I understood that after selecting -ss option, I would see the type of cys as CYS2 in the constructed .gro file as well as in the .top file since the CYS2 name appears in the 8 th and 9 th columns and they are described as the new name for residue A and residue B. So, I should perform a preliminary simulation in order to make the corresponding cysteine residue within the cutoff? -Original Message- From: "Mark Abraham" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Date: Mon, 3 Mar 2008 20:46:15 +1100 (EST) Subject: Re: Re: [gmx-users] procedure for creating an S-S bridge > Thank you Mark, but I am a little bit confused. > > In the link you sent to me, > http://wiki.gromacs.org/index.php/specbond.dat, the disulphide bond is > described in the specbond.dat file (in the first line). However, the > following sentence is written under the given table: > > "To describe new possible special bonds, such as disulfides, so that > pdb2gmx can generate them for you, you should add new lines similar to > these example lines, and update the counter in the first line. " > > So, I understood that the description made within the table does not > describe the Cys-Cys bond. Then, what does it represent? What do you think the second line of the file describes? > After I used the pdb2gmx with -ss option, the type of Cys is given as CYSH > in the .gro file. ... and the pdb2gmx output doesn't report making a special bond, and using pdb2gmx without the -ss option produces the same output. Your conclusion here is...? > So, which one is true? > > Additionaly, I think, this type of information is not enough to create a > disulphide bond. My cysteine residues are not directed to each other for > making a Cys-Cys bond. So, what types of steps do I have to follow ? There > are papers, of course, in which these types of bonds are made, but the > description is not made properly. See the final line of the specbond.dat page. You'll need to change your input structure. Think about distance restraints and a preparatory MD 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 Ozge Engin = Computational Science & Engineering Koc University ___ 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] procedure for creating an S-S bridge
> Thank you Mark, but I am a little bit confused. > > In the link you sent to me, > http://wiki.gromacs.org/index.php/specbond.dat, the disulphide bond is > described in the specbond.dat file (in the first line). However, the > following sentence is written under the given table: > > "To describe new possible special bonds, such as disulfides, so that > pdb2gmx can generate them for you, you should add new lines similar to > these example lines, and update the counter in the first line. " > > So, I understood that the description made within the table does not > describe the Cys-Cys bond. Then, what does it represent? What do you think the second line of the file describes? > After I used the pdb2gmx with -ss option, the type of Cys is given as CYSH > in the .gro file. ... and the pdb2gmx output doesn't report making a special bond, and using pdb2gmx without the -ss option produces the same output. Your conclusion here is...? > So, which one is true? > > Additionaly, I think, this type of information is not enough to create a > disulphide bond. My cysteine residues are not directed to each other for > making a Cys-Cys bond. So, what types of steps do I have to follow ? There > are papers, of course, in which these types of bonds are made, but the > description is not made properly. See the final line of the specbond.dat page. You'll need to change your input structure. Think about distance restraints and a preparatory MD 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: Re: [gmx-users] procedure for creating an S-S bridge
Thank you Mark, but I am a little bit confused. In the link you sent to me, http://wiki.gromacs.org/index.php/specbond.dat, the disulphide bond is described in the specbond.dat file (in the first line). However, the following sentence is written under the given table: "To describe new possible special bonds, such as disulfides, so that pdb2gmx can generate them for you, you should add new lines similar to these example lines, and update the counter in the first line. " So, I understood that the description made within the table does not describe the Cys-Cys bond. Then, what does it represent? After I used the pdb2gmx with -ss option, the type of Cys is given as CYSH in the .gro file. So, which one is true? Additionaly, I think, this type of information is not enough to create a disulphide bond. My cysteine residues are not directed to each other for making a Cys-Cys bond. So, what types of steps do I have to follow ? There are papers, of course, in which these types of bonds are made, but the description is not made properly. Thanks in advance -Original Message- From: "Mark Abraham" <[EMAIL PROTECTED]> To: "Discussion list for GROMACS users" Date: Mon, 3 Mar 2008 10:15:48 +1100 (EST) Subject: Re: [gmx-users] procedure for creating an S-S bridge > Hi all, > > I want to create an S-S bond within my peptide. So, I used the CYSH type > cysteine residue and pdb2gmx with -ss option. However, I saw that the S-S > bridge was formed between the ARG-CYS pair but not between the CYS-CYS > pair. That's not possible with the unmodified form of specbond.dat - you are probably seeing a visualization artefact http://wiki.gromacs.org/index.php/Trajectory_Visualisation#Topology_bonds_vs_Rendered_bonds. > So, I think -ss option with pdb2gmx is not enough to make this bond. What > additional steps do I follow to construct this bond ? Check out http://wiki.gromacs.org/index.php/specbond.dat 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 Ozge Engin = Computational Science & Engineering Koc University ___ 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
