[gmx-users] Error while performing a REMD simulation

Luis Miguel Medina Solano migu-med at uniandes.edu.co
Sat Apr 9 07:34:24 CEST 2011


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??


Luis Miguel Medina Solano
Master student, Chemical Engineering . Universidad de los Andes.
Chemical engineer, Universidad de los Andes.
Biologist, Universidad de los Andes.

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