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

Thu Sep 19 12:24:01 CEST 2013

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
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>> 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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>> >> >> >>
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> > 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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>> >> >>
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Guanglei Cui
>> >> > --
>> >> > gmx-users mailing list    gmx-users at gromacs.org
>> >> > http://lists.gromacs.org/mailman/listinfo/gmx-users
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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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