[gmx-users] precision of input gro file

[Mark Abraham]

Hi,

Yes g96 is a good format for that

Mark

On Thu, 15 Jun 2017 14:38 Yu Ogawa <ayogwa at gmail.com> wrote:

> Hi Mark,
> Thanks for suggestions. I will take a look at the g96 format.
> I try to deform a part of polymer crystal with a small displacement, and
> then relax the structure in MD while keeping the displacement by
> constraint. As the displacement can be very small, I want to have an input
> structure file with a higher precision.
> Thanks!
> Yu
>
> 2017-06-15 13:12 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:
>
> > Hi,
> >
> > Usually one doesn't need a higher precision text file. The g96 format
> does
> > work for this, but you should probably be using a real trajectory or
> > checkpoint format for whatever you are trying to do. That would have been
> > good to describe, rather than assuming the form of the solution ;-)
> >
> > Mark
> >
> > On Thu, 15 Jun 2017 13:10 Yu Ogawa <ayogwa at gmail.com> wrote:
> >
> > > Hi Eric,
> > > Thanks for replying.
> > >
> > > I may be wrong, but what I understand from the online manual is that we
> > > have a higher precision in MD calculation (as in trr file). I am not
> sure
> > > if grompp recognizes a higher precision than 3 decimal places.
> > >
> > > When I did editconf with a gro file with higher precision as an input,
> I
> > > got an output gro file with coordinates rounded to 3 decimal places.
> So I
> > > am a bit doubtful if it's the case with the grompp program.
> > >
> > >
> > > 2017-06-15 11:49 GMT+01:00 Eric Smoll <ericsmoll at gmail.com>:
> > >
> > > > Hello Yu,
> > > >
> > > > Read this carefully.
> > > >
> > > > http://manual.gromacs.org/online/gro.html
> > > >
> > > > As far as I know, Gromacs will accept gro files with high precision
> if
> > > the
> > > > input file follows this format.
> > > >
> > > > Best,
> > > > Eric
> > > >
> > > > > On Jun 15, 2017, at 4:33 AM, Yu Ogawa <ayogwa at gmail.com> wrote:
> > > > >
> > > > > Hello gmx users,
> > > > > Can we increase a precision of input structure file more than 3
> > decimal
> > > > > places?
> > > > > Thank you for your help!
> > > > > Yu
> > > > > --
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