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

Mark Abraham mark.j.abraham at gmail.com
Tue Jun 18 13:07:06 CEST 2013 

gmxcheck will compare .tpr files?


On Tue, Jun 18, 2013 at 12:09 PM, gromacs query <gromacsquery at gmail.com>wrote:

> Dear Mark,
>
> >> You haven't stated your purpose for the information, so it's hard to be
> helpful.
>
> I have two structures in one file. One is using original OPLSAA ("A") and
> other using modified OPLSAA ("B"). While grompping I get over riding params
> which is OK unless "A" and "B" has same angle/dihedral conflict.
>
> regards,
>
>
> On Tue, Jun 18, 2013 at 12:45 PM, Mark Abraham <mark.j.abraham at gmail.com
> >wrote:
>
> > 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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