[gmx-users] Questions about REMD calculations

[Mark Abraham]

  On 15/10/2010 2:54 AM, ABEL Stephane 175950 wrote:
> 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

IMO there are a lot of published REMD studies that use a temperature 
range far in excess of what they really needed. Indeed, there are 
several that were then so short that they didn't get much value for the 
higher-temperature replicas. REMD is useful for enhancing sampling, 
perhaps because barriers are easier to cross at higher temperatures. In 
principle, you want as large a temperature range as will allow you to 
traverse the highest barrier readily. That is rarely known in advance, 
but your expectation of what these peptides will do in the simulation 
should guide you. If they were going to wander around on their own and 
not agglomerate, then a matter of tens of degrees is probably enough :-) 
If they're going to tie knots around each other (a la prions), then 
maybe no reasonable temperature will ever break them up.

Otherwise, I agree with the other posts.

Mark

> 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
> ------------------------------