[gmx-users] Regarding minimum size

[Mark Abraham]

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
> > > >
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>