[gmx-users] Regarding minimum size

[Chhavi Yadav]

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?

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. 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?

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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