[gmx-users] Regarding minimum size

[Mark Abraham]

Hi,

You should really take the time to understand how you set up the
description of a system in the .top file. That content is serialized into
the .tpr file, and present in the gmx_mtop_t type.

The potential energy (and its derivatives, including the force) depend
parametrically on the coordinates, but the functional form is (typically)
constant, described by the above topology.

Mark

On Fri, Mar 16, 2018 at 11:13 PM Chhavi Yadav <cy1235 at nyu.edu> wrote:

> Also,
> You said
>
> "The .tpr provides only the model physics.
>
> It won't work because the .tpr reads a configuration into the state, and
> then rerun reads a different one."
>
> What do you mean by model physics? If I am thinking about it correctly,
> then .tpr should be a file constant for all molecules or is it the physics
> as applicable to a particular molecule? If its the second case then I would
> have to change both .tpr and .gro.
>
> On Fri, Mar 16, 2018 at 6:04 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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