[gmx-users] Error while performing a REMD simulation

devicerandom devicerandom at gmail.com
Sun Apr 10 01:05:34 CEST 2011

On 09/04/11 06:34, Luis Miguel Medina Solano wrote:
> Hello,
> Right now I'm trying to perform a REMD simulation of a poly-alanine
> peptide, using 43 replicas ranging from 300-500 K. the procedure I'm
> using is the following:
> 1. Energy minimization of the peptide in vacuum
> 2. generation of the simulation box. a dodecahedron box.
> 3. filling the simulation box with water.
> 4. EM of the solvated system.
> 5. position restraind MD
> 6. NVT MD (for each replica)
> 7. NPT MD (for each replica)
> 8. REMD at constant T and P.
> my problem is that at the beginning of the REMD the simulation Box y
> displaced, leaving some water molecules outside the simulation box,
> which cause the system to collapse. how can I solve this problem??

I highly doubt that the system is collapsing because molecules are 
"outside the simulation box". I think it's just a visualization problem 
with periodic boundary conditions, unrelated to your issue.

Could you provide us the exact error message (copied and pasted from 
your terminal) for a start, and also the .mdp file?

Is the time step you're using small enough to work at 500K, for example?



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