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

Mark Abraham mark.j.abraham at gmail.com
Wed Sep 18 22:56:13 CEST 2013 

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
>> >> >> >> > --
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>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> > Guanglei Cui
>> >> >> > --
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>> >> >>
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Guanglei Cui
>> >> >
>> >> > --
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>> >
>> >
>> >
>> > --
>> > Guanglei Cui
>> > --
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>
>
>
> --
> Guanglei Cui
> --
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