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

Mark Abraham mark.j.abraham at gmail.com
Wed Sep 18 22:08:01 CEST 2013 

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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>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > 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
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