It is only a simple question, not a criticism of any kind. I'm sure there may be perfect reasons to choose one implementation over another. To someone who is not familiar with the history of gmx development, it is something to be aware of. That's all.
On Wed, Sep 18, 2013 at 4:56 PM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > Implementation and description of a model physics are two different > things. You could compute KE of a particle with 0.5 * m * v^2, but if > the mass is used nowhere else, why wouldn't you pre-multiply the mass > by 0.5? > > Mark > > On Wed, Sep 18, 2013 at 4:31 PM, Guanglei Cui > <amber.mail.arch...@gmail.com> wrote: > > 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 > -- > 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
