[gmx-users] to print parameters used from force field

[Mark Abraham]

grompp does this kind of parsing and pruning while producing the .tpr file,
and the result can be dumped with gmxdump. Each interaction type that is
used is listed and the sets of parameters are also listed and the
cross-reference is made. But it is not really intended for human digestion.
You haven't stated your purpose for the information, so it's hard to be
helpful.

Mark


On Tue, Jun 18, 2013 at 11:13 AM, gromacs query <gromacsquery at gmail.com>wrote:

> Dear Florian,
>
> I used -pp as you suggested but it dumps every thing from oplsaa (this is
> FF I am using). So may be I think this gives an output which can be used as
> an independent file, as it includes everything, instead of directing to
> oplsaa.ff directory.
>
> But still am not getting to print params for desired atomtypes in system.
>
> regards,
>
>
> On Tue, Jun 18, 2013 at 11:57 AM, Florian Dommert <
> dommert at icp.uni-stuttgart.de> wrote:
>
> > Hi,
> >
> >  I just recently learned from the mailing list that there is an -pp
> option
> > in grompp, which should write all parameters into a single top file.
> > Haven't
> > tried it yet, but it should work.
> >
> > /Flo
> >
> > -------
> > Dr. rer. nat. Florian Dommert
> >
> > Institut für Computerphysik
> > Universität Stuttgart
> > Allmandring 3
> > D-70569 Stuttgart
> >
> > Tel.: 0711-68563613
> > Fax: 0711-68563658
> >
> > > -----Ursprüngliche Nachricht-----
> > > Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> > > bounces at gromacs.org] Im Auftrag von gromacs query
> > > Gesendet: Dienstag, 18. Juni 2013 10:42
> > > An: Discussion list for GROMACS users
> > > Betreff: Re: [gmx-users] to print parameters used from force field
> > >
> > > Dear Mark,
> > >
> > >
> > > >> Grep?
> > >
> > > Sorry but I mean to say I have say .itp file like this
> > >
> > > [ bonds ]
> > > ;   ai     aj    funct    c0    c1    c2    c3
> > >      1      2    1
> > > and so on....
> > >
> > > [ angles ]
> > > ;   ai     aj     ak    funct    c0    c1    c2    c3
> > >      2      1      3    1
> > > and so on.....
> > >
> > > So I want to extract params from oplsaa for all these. Or do I need to
> > map
> > > atom types for these atom numbers then only I can extract or is there
> any
> > > inbuilt Gromacs module in this regard
> > >
> > > regards,
> > >
> > >
> > >
> > > On Tue, Jun 18, 2013 at 11:32 AM, Mark Abraham
> > > <mark.j.abraham at gmail.com>wrote:
> > >
> > > > Grep?
> > > > On Jun 18, 2013 10:23 AM, "gromacs query" <gromacsquery at gmail.com>
> > > wrote:
> > > >
> > > > > Dear All,
> > > > >
> > > > > Is there any way to print parameters used for system (just for the
> > > > > atomtypes present in system). I have all necessary files (top, tpr,
> > gro
> > > > and
> > > > > oplsa.ff)
> > > > >
> > > > > regards,
> > > > > Jiom
> > > > > --
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