[gmx-users] pbc nojump with replica exchange behaves differently than with regular MD

[Justin Lemkul]

On 11/28/19 9:44 AM, Ramon Crehuet wrote:
> Dear all,
> As a follow-up to my question, I have seen that in a regular MD, the coordinates of the original trajectory are always smaller than the unitcell vectors, whereas this is not true in the trajectory from the replica exchange (deviations up to 1.5%). Could this be confusing trajconv?
> Could it be that in an exchange attempt only the coordinates of the atoms are exchanged between temperatures but not the box size? (the dynamics use a Parrinello-Rahman barostat).

The entire state is exchanged (at least in the current version of the 
code that I'm looking at), so the box and everything else gets swapped.

For a simple system of solute in water, you should be able to just do 
trjconv -pbc mol -center without all the intermediate steps (-pbc whole, 
-pbc nojump, etc). I suspect -pbc nojump won't work because you do not 
have a continuous trajectory during REMD, so the coordinates may change 
quite dramatically between snapshots, leading to a breakdown in the 
algorithm.

-Justin

> Thanks again.
> All the best,
> Ramon
>
> ----- On 28 Nov, 2019, at 11:49, Ramon Crehuet <ramon.crehuet at iqac.csic.es> wrote:
>
>> Dear all,
>> I have run a temperature replica exchange and I would like to analyze the
>> resulting trajectory for a given temperature (i.e. not following a replica
>> across temperatures using demux.pl).
>> The simulations consist of a single protein chain. I can easily generate have a
>> whole molecule, named `whole.pdb`.
>> When I was running regular MD, the following worked fine to generate whole
>> structures that diffused out of the box:
>> gmx trjconv -f md.xtc -s whole.pdb -pbc nojump -o whole.xtc
>> But repeating that for one of the md.xtc of the replica exchange does not work.
>> Each atom diffuses or of the box (i.e. without jumps) but to different
>> directions, resulting in an apparently exploding molecule.
>> Should there be a different treatment of RE simulations? If so, what should I
>> do? (I have tried the -pbc nojump step followed or preceded by -pbc whole
>> without success).
>> Thanks for your attention.
>> Best,
>> Ramon

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Justin A. Lemkul, Ph.D.
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