[gmx-users] How to compute self diffusivities when the xtc trajectory file contains only a subset of atoms

[Mark Abraham]

On Sun, Sep 28, 2014 at 5:36 PM, rocwhite168 <rocwhite168 at 163.com> wrote:

> Hi Mark,
>
> Thanks for your suggestion. That's actually what I've been doing. However,
> it requires modifying not only .top but also conf.gro and grompp.mdp (to
> remove reference to index groups of fixed atoms that no longer exist), as
> well as rerunning make_ndx. I was hoping there would be a less tortuous
> path :)


Sounds like a 10 minute job to me :-) - sed on the gro file, wc -l to check
the number of atoms, text editor to pull out any references in the .mdp
that no longer make sense. You only need the topology definitions in the
.tpr, not anything to do with the physics...

It's strange that .tpr generated by grompp has everything correctly:
>
>    moltype (0):
>       name="Water"
>       atoms:
>          atom (4):
> ...
>          atom (4):
>             atom[0]={name="OW"}
>             atom[1]={name="HW"}
>             atom[2]={name="HW"}
>             atom[3]={name="MW"}
>          type (4):
> ...
>
> but .tpr generated by gmx convert-tpr does not:
>
>    moltype (0):
>       name="This becomes the system name"
>       atoms:
>          atom (60):
> ...
>          atom (60):
>             atom[0]={name="OW"}
>             atom[1]={name="HW"}
>             atom[2]={name="HW"}
>             atom[3]={name="MW"}
>             atom[4]={name="OW"}
>             atom[5]={name="HW"}
>             atom[6]={name="HW"}
>             atom[7]={name="MW"}
>             atom[8]={name="OW"}
>             atom[9]={name="HW"}
>             atom[10]={name="HW"}
>             atom[11]={name="MW"}
>             atom[12]={name="OW"}
> ...
>
> Any ideas why this would happen?
>

Like most software, because someone made it work well enough to solve their
immediate problem.

Back on the main question, why aren't you just using index groups on the
trajectory with the tool you were planning to use? That's the simplest time
to take a subset.

Mark


> Thanks,
>
> Roc
>
> On Sun, Sep 28, 2014 at 1:32 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > I'm not sure this will help, because I'm not sure what the origin of the
> > problem is, but you can easily hack a copy of your .top so that a fresh
> run
> > of grompp will produce a .tpr that will match the .xtc.
> >
> > Mark
> > On Sep 28, 2014 7:47 AM, "rocwhite168" <rocwhite168 at 163.com> wrote:
> >
> > > Dear GROMACS users,
> > >
> > > I'm trying to compute mean square displacements for molecules. My
> > > system contains atoms that don't move, so I used "compressed-x-grps"
> > > in grompp.mdp to exclude them from the xtc trajectory file. After
> > > mdrun, I ran "gmx convert-tpr -s topol.tpr -n index.ndx" to reduce the
> > > set of atoms in the tpr file to match those in the xtc file (otherwise
> > > "gmx msd" will fail because the atom indices exceed those found in the
> > > xtc file). Say, for both "compressed-x-grps" and "gmx convert-tpr" I
> > > specified OW_HW to include all water molecules. However, tpxout.tpr
> > > generated by "gmx convert-tpr" treats all water molecules as a large,
> > > single molecule, and as a result "gmx msd" detects only that one
> > > molecule. This would be useful for computing corrected diffusivities,
> > > but is there a way to let "gmx msd" detect individual molecules
> > > correctly if I want to compute self diffusivities?
> > >
> > > Any suggestions would be very much appreciated!
> > >
> > > Thanks,
> > >
> > > Roc
> > > --
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