[gmx-users] trjconv, pbc and breaking of multiple peptides

ms devicerandom at gmail.com
Wed Nov 10 23:43:00 CET 2010

On 10/11/10 22:28, Justin A. Lemkul wrote:
>> First, let me see if I understand it correctly. From your explanation
>> (and intuition), it seems that the issue is that "center of mass" in a
>> periodic environment is ambiguous -there are always (at least) two
>> alternate configurations that have the center of mass at the center of
>> the box any time, and -center doesn't necessarily choose the most
>> compact one (i.e. the one where the box center is closest on average
>> to atoms). So, for example, in a 1-D periodic environment, this:
>> ... O|O O|O ...
>> is equivalent to this
>> | OO | OO ...
>> the center of mass between the O's being always at the center of the
>> box in both cases.
> Correct.
>> But I don't see how choosing one residue could help -I mean, the
>> residues wander practically everywhere in the box during the
>> simulation and none of them is privileged ; I don't see why centering
>> only around one would be better. It could help if they were only two,
>> but we talk of eight objects here (and possibly many more in the
>> future)...
>> ...now I see it: You mean that, since I force to center around one of
>> the objects, and if on average it should belong to the cluster, the
>> whole thing should be more often than not within the box?
> That's it. Take, for example, peptides A, B, and C. Peptide A is a
> nucleation point for B and C to attach. Conceivably, trjconv could
> choose a "center" that involves C on one "side" of the box and A+B on
> the other. The whole protein is still "centered" by its criteria.
> If, physically, A is in the core of the aggregate, then I could choose
> some residue in peptide A and choose to center about it. There is no
> other alignment that trjconv can assign, other than to place that chosen
> residue of peptide A right in the middle of your unit cell. It can't be
> broken any other way.

It seems to work right this time! Beautiful trick. Thank you again so 
much -if I could, I would give you a big hug. I am still a newbie with 
molecular simulations (my Ph.D. was on experimental biophysics) and I 
still fall into a lot of easy traps!


Massimo Sandal, Ph.D.

More information about the gromacs.org_gmx-users mailing list