[gmx-users] Regarding minimum size

[Chhavi Yadav]

Thanks a lot!

Is there a function similar to

read_tpx_state that reads the .gro file and in which function is it
being called? I couldn't find it.


On Fri, Mar 16, 2018 at 5:51 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> On Fri, Mar 16, 2018 at 10:43 PM Chhavi Yadav <cy1235 at nyu.edu> wrote:
>
> > Hello,
> >
> > So here is what I want to do. Kindly help.
> >
> > I generate .gro and .top from .pdb file using pdb2gmx command. Then using
> > .gro and .top I generate .tpr with the grompp command. Then using .tpr
> and
> > .gro files I generate the .edr file using mdrun -rerun.
> >
> > Issue 1: When I change the coordinates of some random atoms only in the
> > .gro file, I see a corresponding change in the potential energy of the
> > molecule after running mdrun.(Let us ignore the fact that randomly
> changing
> > the atom coordinates is not the right thing to do). Should I be changing
> > both .tpr and .gro files to see the valid change? Is only changing .gro
> > enough and why?
> >
>
> You're doing a rerun, so the coordinates come from the file you pass to
> -rerun. The .tpr provides only the model physics.
>
> Issue 2:I want to find the potential energy of different molecules in a
> > loop but I do not want to read the molecules from their .gro files. I
> want
> > to read one .gro file in the beginning, find its potential energy and
> then
> > want to iteratively change the already stored topology of the previous
> > molecule and find the new corresponding potential energy.
>
>
> You can't do that at the level you tried. EIther pre-generate the
> coordinates you want in a trajectory file you pass to -rerun (strongly
> recommended) or modify how rerun works to instead vary the coordinates.
>
>
> > I tried
> > accomplishing this by calling mdrun once in the beginning with the
> original
> > .gro and .tpr files, then I changed the coordinates of some atoms
> modifying
> > values in t_state.
> > But when I call mdrun again with the t_state changes, I get the potential
> > energy of the previous molecule instead, even when I made changes to only
> > read the .gro once in the beginning and never again. Can you please
> explain
> >
>
>
> > why are the changes in t_state being overlooked?
> >
>
> It won't work because the .tpr reads a configuration into the state, and
> then rerun reads a different one.
>
> I strongly suggest you get your method to work on unmodified GROMACS
> passing creative files to -rerun, and only once you know what the correct
> results are, *and* you need the control and/or performance benefit move to
> some modified form of the source code.
>
> Mark
>
> Thanks,
> > Chhavi
> >
> >
> > On Fri, Mar 16, 2018 at 4:53 PM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > Change the contents of the file on disk... Again, whatever you are
> trying
> > > to do should be approached in a totally different way.
> > >
> > > Mark
> > >
> > > On Fri, Mar 16, 2018 at 9:43 PM Chhavi Yadav <cy1235 at nyu.edu> wrote:
> > >
> > > > I basically want to change the atom coordinates in the variable where
> > the
> > > > gro file contents are read and stored. So I want to change the
> contents
> > > of
> > > > that variable.
> > > >
> > > > On Fri, Mar 16, 2018 at 4:39 PM, Chhavi Yadav <cy1235 at nyu.edu>
> wrote:
> > > >
> > > > > Hello,
> > > > >
> > > > > I wanted to know which function calls another function(which one is
> > > this
> > > > > too) that prints the following:
> > > > >
> > > > > starting md rerun 'LYSOZYME', reading coordinates from input
> > trajectory
> > > > > '1aki/1AKI.gro'
> > > > >
> > > > > Reading frames from gro file 'LYSOZYME;', 1960 atoms.
> > > > >
> > > > > Reading frame       0 time    0.000
> > > > >
> > > > > Kindly help.
> > > > >
> > > > > Regards,
> > > > > Chhavi
> > > > >
> > > > >
> > > > --
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