[gmx-users] precision of input gro file

[Yu Ogawa]

Hi Mark,
Great! Thanks a lot. I try with the g96 format.
Best, -Yu

2017-06-15 15:04 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:

> 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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