[gmx-users] Questions about REMD calculations

[chris.neale at utoronto.ca]

Stefane,

for more information on what Mark is talking about here, check out his  
publication:

M. J. Abraham and J. E. Gready (2008) "Ensuring Mixing Efficiency of
Replica-Exchange Molecular Dynamics Simulations" J. Chem. Theory Comput.
(4), 1119-1128.

> 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