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
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