[gmx-users] Regarding minimum size

[Mark Abraham]

Hi,

do_md() has a boolean about rerun that controls whether it calls the
function that reads from the trajectory file

Mark

On Fri, Mar 16, 2018 at 11:06 PM Chhavi Yadav <cy1235 at nyu.edu> wrote:

> 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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