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
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