[gmx-users] issue in replica exchange

XAvier Periole x.periole at rug.nl
Thu Apr 25 13:28:00 CEST 2013


I have been recently using the REMD code in gmx-407 and gmx-453 and got a few systems crashing for unclear reasons so far. The main tests I made are using gmx407 but it is all reproducible with gmx453. The crashing was also reproduced (not necessarily at the same time point) on several architectures. 

The system is made of a pair of proteins in a membrane patch and for which the relative orientation is controlled by non-native bond/angles/dihedrals to perform an umbrella sampling. I use the MARTINI force field but that might not be relevant here. 

The crashes occur following exchanges that do not seem to occur the correct way and preceded by pressure scaling warnings … indicative of a strong destabilisation of the system and eventual explosion. Some information seems to be exchanged inaccurately. 

Trying to nail down the problem I got stuck and may be some one can help. I placed a pdf file showing plots of bonded/nonbonded energies, temperatures, box size etc … around an exchange that does not lead to a crash (here: md.chem.rug.nl/~periole/remd-issue.pdf). I plotted stuff every step with the temperature colour coded as indicated in the first figure. 

From the figure it appears that the step right after the exchange there is a huge jump of Potential energy coming from the LJ(SR) part of it. Although there are some small discontinuities in the progression of the bond and angle energy around the exchange they seem to fine. The temperature and box size seem to respond to it a few step latter while the pressure seems to be affected right away but potentially as the Epot will affect the viral and thus the Pressure. 

The other potential clue is that the jumps reduce with the strength of the pressure coupling. A 1/2 ps tau_p (Berendsen) will lead to a crash while a 5/10/20 ps won't. Inspection of the time evolution of the Epot, box … indicates that the magnitude of the jumps is reduced and the system ca handle the problem. 

One additional info since I first posted the problem (delayed by the file first attached but now given with a link) the problem is accentuated when the replicas differ in conformation. I am looking at the actual differences as you'll read this email.

That is as far as I could go. Any suggestion is welcome.

MD-Group / Univ. of Groningen
The Netherlands

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