[gmx-users] Questions about REMD calculations

ABEL Stephane 175950 Stephane.ABEL at cea.fr
Thu Oct 14 17:54:02 CEST 2010

Dear all, 
I come back to you for several questions about the futures replica-exchange calculations that i would like to perform. The system of interest will contain 12 peptides (with 7 residues each) and 40000 water molecules, it come from a previous MD performed in NPT ensemble. With these systems, i would like to study the aggregation process between the peptides.
After reading several paper about REMD method and playing with the Temperature generator for REMD-simulations web server (http://folding.bmc.uu.se/remd/), i suspect that this system is too big for REMD. Indeed if use the following parameters in the webserver
Pdes 0.2
Temperature range 290 - 600
Number of water molecules 41380
Number of protein atoms 1092
Including all H ~ 1656
Number of hydrogens in protein ~ 240
Number of constraints ~ 1092
Number of vsites ~ 0
Number of degrees of freedom ~ 250464
Energy loss due to constraints 520.59 (kJ/mol K)

I obtain 271 replicas (ouch !!) . If i assume that for each replica app. 16 CPU, The simulations will be too big and will cost a lot CPU time. 
So my question is can i reduce safely the number of water in system to reduce the number of replicas ? 
For example for 10000 mol of water the number of replicas will be 135. It is not bad. It is a good option to overcome this limitation. 

I have also read the number of replicas can be significantly reduced by using variants of REMD for example replica exchange with solute tempering (REST) from Berne and co-workers. Is this method is implemented in GROMACS ?
Or Can i use the REMD in implicit solvant for example with the coarse grain OPEP force field as described in Chebaro, et al. (2008).J. Phys. Chem. B 113(1): 267-274. or by Wang and Voth in J. Phys. Chem. B 112(41): 13079-13090. 
Any advices and comments are welcome 
Stéphane Abel, PhD
91191 Saclay, FRANCE
website: http://www.st-abel.com

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