hmm, does that mean the gmx force field file format or specifications are not backward compatible?
On Wed, Sep 18, 2013 at 4:08 PM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > There are technical differences between versions about how the VDW > parameters are computed. You should not expect .tpr equivalence > between minor version changes such as 4.0 and 4.6. You need to compile > a 4.0.x grompp to see if your setup is equivalent, but having done so > you should be able to use the same inputs to 4.6 grompp and get a > correct simulation with 4.6 mdrun. > > Mark > > On Wed, Sep 18, 2013 at 1:55 PM, Guanglei Cui > <amber.mail.arch...@gmail.com> wrote: > > Thanks. gmxcheck is quite helpful. Here is part of the output. It turns > out > > the difference is mainly in the force field parameters, which indicates > the > > top file provided may not be the one used to produce the tpr file. > Perhaps > > it is best to contact the authors, unless the difference is due to > certain > > changes between gmx 4.0.x and gmx 4.6.3. > > > > inputrec->nsteps (50000000 - 5000) > > inputrec->nstcalclr (5 - 0) > > inputrec->nstdhdl (1 - 50) > > inputrec->fepvals->init_fep_state ( 0.000000000e+00 - -1.000000000e+00) > > inputrec->fepvals->lambda_neighbors[1] (0 - 1) > > inputrec->fepvals->sc_power (0 - 1) > > inputrec->dihre_fc (1.000000e+03 - 0.000000e+00) > > inputrec->grpopts.ngtc (4 - 1) > > inputrec->grpopts.ngener (4 - 1) > > inputrec->grpopts.nrdf[ 0] (8.610900e+04 - 2.136210e+05) > > idef->iparam[12]1: c6= 4.23112651e-03, c12= 4.76949208e-06 > > idef->iparam[12]2: c6= 4.68938737e-08, c12= 1.15147106e-12 > > idef->iparam[54]1: c6= 4.58155479e-03, c12= 4.48611081e-06 > > idef->iparam[54]2: c6= 4.46544206e-08, c12= 8.37594751e-13 > > idef->iparam[82]1: c6= 3.75142763e-03, c12= 4.22875655e-06 > > idef->iparam[82]2: c6= 4.15773336e-08, c12= 1.02092445e-12 > > idef->iparam[96]1: c6= 3.83810000e-03, c12= 2.83264171e-06 > > idef->iparam[96]2: c6= 2.83739432e-08, c12= 3.04270091e-13 > > idef->iparam[124]1: c6= 4.26879199e-03, c12= 3.50070763e-06 > > idef->iparam[124]2: c6= 3.50897622e-08, c12= 4.64908439e-13 > > idef->iparam[152]1: c6= 3.59375845e-03, c12= 2.76020933e-06 > > idef->iparam[152]2: c6= 2.76677472e-08, c12= 3.21553060e-13 > > idef->iparam[166]1: c6= 7.79988989e-03, c12= 1.19875567e-05 > > idef->iparam[166]2: c6= 1.12529349e-07, c12= 4.90395051e-12 > > idef->iparam[168]1: c6= 4.23112651e-03, c12= 4.76949208e-06 > > idef->iparam[168]2: c6= 4.68938737e-08, c12= 1.15147106e-12 > > idef->iparam[171]1: c6= 4.58155479e-03, c12= 4.48611081e-06 > > idef->iparam[171]2: c6= 4.46544206e-08, c12= 8.37594751e-13 > > idef->iparam[173]1: c6= 3.75142763e-03, c12= 4.22875655e-06 > > idef->iparam[173]2: c6= 4.15773336e-08, c12= 1.02092445e-12 > > idef->iparam[174]1: c6= 3.83810000e-03, c12= 2.83264171e-06 > > idef->iparam[174]2: c6= 2.83739432e-08, c12= 3.04270091e-13 > > idef->iparam[176]1: c6= 4.26879199e-03, c12= 3.50070763e-06 > > idef->iparam[176]2: c6= 3.50897622e-08, c12= 4.64908439e-13 > > idef->iparam[178]1: c6= 3.59375845e-03, c12= 2.76020933e-06 > > idef->iparam[178]2: c6= 2.76677472e-08, c12= 3.21553060e-13 > > idef->iparam[179]1: c6= 7.79988989e-03, c12= 1.19875567e-05 > > idef->iparam[179]2: c6= 1.12529349e-07, c12= 4.90395051e-12 > > idef->iparam[180]1: c6= 6.22385694e-03, c12= 5.03394313e-06 > > idef->iparam[180]2: c6= 2.05496373e-24, c12= 0.00000000e+00 > > idef->iparam[181]1: c6= 3.93928867e-03, c12= 3.50622463e-06 > > idef->iparam[181]2: c6= 3.50750256e-08, c12= 5.46337281e-13 > > idef->iparam[194]1: c6= 3.93928867e-03, c12= 3.50622463e-06 > > idef->iparam[194]2: c6= 3.50750256e-08, c12= 5.46337281e-13 > > ... > > > > > > On Wed, Sep 18, 2013 at 10:14 AM, Mark Abraham <mark.j.abra...@gmail.com > >wrote: > > > >> That -om mechanism has been broken for about a decade, unfortunately. > >> > >> You will need to include the file, or post a link a file, not attach > >> it, if you want users of this list to see it. > >> > >> gmxcheck to compare your new and old .tpr files is useful to see what > >> you might need in the new .mdp file to reproduce the first one. Note > >> that grompp -c yourold.tpr is the best way to get the same starting > >> coordinates. > >> > >> Mark > >> > >> On Wed, Sep 18, 2013 at 3:48 PM, Guanglei Cui > >> <amber.mail.arch...@gmail.com> wrote: > >> > gmxdump -om writes out a mdp file based on the tpr, but that is not > read > >> by > >> > grompp. I tried to change or comment out mdp options that are not > >> > recognized by grompp. It is attached here. The simulation soon crashes > >> with > >> > LINCS errors after 25 steps, while the original tpr runs properly. I'm > >> not > >> > sure what's missing here. > >> > > >> > > >> > On Tue, Sep 17, 2013 at 6:12 PM, Mark Abraham < > mark.j.abra...@gmail.com > >> >wrote: > >> > > >> >> No. Theoretically useful, but not implemented. > >> >> > >> >> Mark > >> >> > >> >> On Tue, Sep 17, 2013 at 4:45 PM, Guanglei Cui > >> >> <amber.mail.arch...@gmail.com> wrote: > >> >> > Thanks. Is it possible to dump the parameters in the tpr file to a > mdp > >> >> file? > >> >> > > >> >> > > >> >> > On Tue, Sep 17, 2013 at 3:20 PM, Mark Abraham < > >> mark.j.abra...@gmail.com > >> >> >wrote: > >> >> > > >> >> >> mdrun -nsteps in 4.6 overrides the number of steps in the .tpr > >> >> >> > >> >> >> Mark > >> >> >> > >> >> >> On Tue, Sep 17, 2013 at 8:55 PM, Guanglei Cui > >> >> >> <amber.mail.arch...@gmail.com> wrote: > >> >> >> > Dear GMX users, > >> >> >> > > >> >> >> > I'm new to Gromacs. So apologies if this question is too simple. > >> >> >> > > >> >> >> > I downloaded top/tpr files from the supplementary material of a > >> >> published > >> >> >> > paper. The nsteps set in the tpr file is 100ns. I wish to do a > >> small > >> >> test > >> >> >> > run. Is there any way I can modify that? I've tried to create a > mdp > >> >> file > >> >> >> > that best matches the parameters found through gmxdump, but it > >> gives > >> >> me a > >> >> >> > lot of LINCS error. I can upload the mdp file and gmxdump file > if > >> you > >> >> are > >> >> >> > kind to help. Thanks in advance. > >> >> >> > > >> >> >> > Best regards, > >> >> >> > -- > >> >> >> > Guanglei Cui > >> >> >> > -- > >> >> >> > gmx-users mailing list gmx-users@gromacs.org > >> >> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users > >> >> >> > * Please search the archive at > >> >> >> http://www.gromacs.org/Support/Mailing_Lists/Search before > posting! > >> >> >> > * Please don't post (un)subscribe requests to the list. Use the > >> >> >> > www interface or send it to gmx-users-requ...@gromacs.org. > >> >> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> >> >> -- > >> >> >> gmx-users mailing list gmx-users@gromacs.org > >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> >> >> * Please search the archive at > >> >> >> http://www.gromacs.org/Support/Mailing_Lists/Search before > posting! > >> >> >> * Please don't post (un)subscribe requests to the list. Use the > >> >> >> www interface or send it to gmx-users-requ...@gromacs.org. > >> >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> >> >> > >> >> > > >> >> > > >> >> > > >> >> > -- > >> >> > Guanglei Cui > >> >> > -- > >> >> > gmx-users mailing list gmx-users@gromacs.org > >> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users > >> >> > * Please search the archive at > >> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> >> > * Please don't post (un)subscribe requests to the list. Use the > >> >> > www interface or send it to gmx-users-requ...@gromacs.org. > >> >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> >> -- > >> >> gmx-users mailing list gmx-users@gromacs.org > >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> >> * Please search the archive at > >> >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> >> * Please don't post (un)subscribe requests to the list. Use the > >> >> www interface or send it to gmx-users-requ...@gromacs.org. > >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> >> > >> > > >> > > >> > > >> > -- > >> > Guanglei Cui > >> > > >> > -- > >> > gmx-users mailing list gmx-users@gromacs.org > >> > http://lists.gromacs.org/mailman/listinfo/gmx-users > >> > * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> > * Please don't post (un)subscribe requests to the list. Use the > >> > www interface or send it to gmx-users-requ...@gromacs.org. > >> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> -- > >> gmx-users mailing list gmx-users@gromacs.org > >> http://lists.gromacs.org/mailman/listinfo/gmx-users > >> * Please search the archive at > >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > >> * Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to gmx-users-requ...@gromacs.org. > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > > > > > > > > -- > > Guanglei Cui > > -- > > gmx-users mailing list gmx-users@gromacs.org > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > * Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to gmx-users-requ...@gromacs.org. > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Guanglei Cui -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists