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 Stefane ------------------------------ Stéphane Abel, PhD CEA Saclay DSV/IBITEC-S/SB2SM 91191 Saclay, FRANCE website: http://www.st-abel.com ------------------------------ -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
