[gmx-users] How to compute self diffusivities when the xtc trajectory file contains only a subset of atoms
Mark Abraham
mark.j.abraham at gmail.com
Sun Sep 28 21:05:40 CEST 2014
On Sun, Sep 28, 2014 at 8:32 PM, rocwhite168 <rocwhite168 at 163.com> wrote:
> On Sun, Sep 28, 2014 at 12:24 PM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > 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...
> >
> > Well, 10 min for one state point, and there are multiple temperatures,
> pressures and mixture compositions ... Not that I'm really going to do this
> manually, but facing the impressive set of auxiliary tools Gromacs has, I
> was hoping that I missed a simpler solution.
At some point in research, you have to do it yourself, because nobody else
has done exactly that. :-) In MD, that often means some kind of script. I
must still be missing something, though, because if all you need is a .tpr
that matches your simulation's compressed-x group, then the .mdp is common
to all such simulation analyses, you already have the input .gro file to
use sed on because you used it for the original grompp, and those and the
.top files are common to all simulations with the same composition.
> 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.
> >
> If I just give the original .tpr and .ndx to "gmx msd", the program will
> crash with a segmentation error because the indices for the atoms in the
> index group I want to analyze are larger than the total number of atoms in
> the .xtc file.
>
... you're using gmx msd -mol?
Mark
> >
> > Mark
> >
> > In any case, thanks for your input.
>
> Roc
>
> >
> > > 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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