[gmx-users] modify nsteps in an existing tpr file

Guanglei Cui amber.mail.archive at gmail.com
Thu Sep 19 16:20:25 CEST 2013 

Thanks, Mark.

Just compiled gmx 4.0.5 and created tpr with the 'published' topology file.
Ver. 4.0.5 seems to be the version that was used to create the 'published'
tpr file. The only differences now that matter are these c6 and c12 terms.

Is there any mdp options that may change how c6 and c12 are calculated? I
see this ndelta from gmxdump, regardless the versions, but I can't seem to
map it to an mdp option from the manual.



On Thu, Sep 19, 2013 at 6:24 AM, Mark Abraham <mark.j.abraham at gmail.com>wrote:

> Indeed - your question was fair, and no undue criticism pertained! :-)
> If you are trying to reproduce something, you must expect .tpr
> differences between 4.0.x and 4.6.y. I illustrated the change that has
> taken place in how VDW parameters are used internally in 4.6, and how
> that is distinct from the (presumably) unchanged description of those
> parameters. How and where to document this kind of thing so that
> people who need it can find it and those who don't need it don't drown
> in paper is an impossible problem!
>
> Cheers,
>
> Mark
>
> On Wed, Sep 18, 2013 at 8:34 PM, Guanglei Cui
> <amber.mail.archive at gmail.com> wrote:
> > 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.abraham at 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.archive at 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.abraham at 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.archive at 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.abraham at 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.archive at 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.abraham at gmail.com
> >> >> >> >wrote:
> >> >> >> >
> >> >> >> >> No. Theoretically useful, but not implemented.
> >> >> >> >>
> >> >> >> >> Mark
> >> >> >> >>
> >> >> >> >> On Tue, Sep 17, 2013 at 4:45 PM, Guanglei Cui
> >> >> >> >> <amber.mail.archive at 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.abraham at 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.archive at 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 at gromacs.org
> >> >> >> >> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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> >> >> posting!
> >> >> >> >> >> > * Please don't post (un)subscribe requests to the list.
> Use
> >> the
> >> >> >> >> >> > www interface or send it to gmx-users-request at gromacs.org
> .
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> >> >> >> >> >> --
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> >> >> >> >> >>
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> > --
> >> >> >> >> > Guanglei Cui
> >> >> >> >> > --
> >> >> >> >> > gmx-users mailing list    gmx-users at gromacs.org
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> >> >> >> >> --
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> >> >> >> >>
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> > --
> >> >> >> > Guanglei Cui
> >> >> >> >
> >> >> >> > --
> >> >> >> > gmx-users mailing list    gmx-users at gromacs.org
> >> >> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> >> >> > * Please search the archive at
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> posting!
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> >> >> >> --
> >> >> >> gmx-users mailing list    gmx-users at gromacs.org
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> >> >> >>
> >> >> >
> >> >> >
> >> >> >
> >> >> > --
> >> >> > Guanglei Cui
> >> >> > --
> >> >> > gmx-users mailing list    gmx-users at gromacs.org
> >> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> >> >> > * Please search the archive at
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> >> >> --
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> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > Guanglei Cui
> >> > --
> >> > gmx-users mailing list    gmx-users at gromacs.org
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> >
> >
> >
> > --
> > Guanglei Cui
> > --
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-- 
Guanglei Cui

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