[gmx-users] error comm-grps=Protein SOL

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 8 01:20:47 CEST 2008

Quoting "M. Emal Alekozai" <memala at gmx.net>:

> Hi,
>  >>2. If the option "comm-grps = Protein SOL" physical means (1b) what do
>  >>I have to change in my simulation setup to avoid the warnings/ error
>  >>"T-cm: inf" in the log files?
>  >>
>  >comm-grps = System (as you noted, it does not give the error!)
> I forgot to mention that my system contains except the group "Protein"
> and "SOL" also other groups/ atoms.
> If I would select "System" all the atoms would be considered in the
> center of mass calculation and not only the atoms of the group "Protein"
> and "SOL" :-( .
> There is a large set of old short trajectories which where simulated
> with the settings "comm-grps = Protein SOL".
> I want to create a longer trajectory with the same settings and compare
> it with the old short trajectories.
> If I use in the new long simulation the setting "comm-grps = System" I
> would most likely get a different physical system. The comparison of the
> old short trajectories and the new long trajectory would most ilkley be
> biased because of the different parameters.

If you're only applying COM motion removal to part of the system, I would think
that would lead to some seriously non-physical results.  There is a post from a
while ago (can't remember who said it or what it was in reference to, so bear
with me) that said applying COM motion removal to only the protein (as the
example) was a terrible thing to do and should never be done!  Think about two
molecules in a system - if one continually has its position continually
re-scaled based on COM motion, and the other does not, don't you think the
result will be biased?

The short trajectories probably worked because they didn't run long enough to
encounter the error you're seeing, which will happen when groups collide.

> I can't use for the long simulation the settings "comm-grps = Protein
> SOL" because the log files would fill up my harddisk before the
> simulation really starts.

That should tell you there is a problem in applying those settings to your
system (reference my previous reply).

> Any help to solve this dilemma is welcome :-) .

What might be worthwhile is running some of your "old" systems with comm-grps =
System (and everything else the same) and seeing if the behavior of the system
is substantially different.


> Thanks Emal
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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