[gmx-users] Regarding minimum size

[Chhavi Yadav]

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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