[gmx-users] Questions about REMD calculations
x.periole at rug.nl
Thu Oct 14 18:32:44 CEST 2010
Well indeed the more atoms (degrees of freedom) in your system the
more replicas you need to insure exchanges between temperatures ...
I would say that even 135 replicas * 16 cpus= 2160 cpus ... that is
an enormous amount of cpu time for 12 small peptides :))
do you need to go up to 600K ? You can be sure that at that temperature
the force field is not accurate and the peptides will just be really
what about you keep the temperature lower than 400 K. You still will
increase your sampling considerably but need much less cpus! You can
convince yourself by simulating your system at 400K and 600K and
look at its behavior ...
Then I am not a fan of implicit solvents so I'll pass on that, then
coarse grained FF the OPEP FF seem to be fine for your application.
You can also look at the ones from Deserno's group (bereau-2009) and
from Feig's group (primo: gopal-2010). I am no sure how the one of voth
is transferable ... the others are :))
On Oct 14, 2010, at 9:54 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
> 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
> 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
> CEA Saclay DSV/IBITEC-S/SB2SM
> 91191 Saclay, FRANCE
> website: http://www.st-abel.com
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