On Tue, 2014-05-13 at 17:35 +0530, Saikat Dutta Chowdhury wrote:
> Hi,
> I ran a REMD of a small peptide in implicit solvent for 16 replicas.
>
> My general mdin file is as follows:
>
> Equilibration
> &cntrl
> * irest=1, ntx=5,*
> nstlim=10000, dt=0.002,
> ntt=3, gamma_ln=1.0,
> temp0=XXXXX, ig=RANDOM_NUMBER,
> ntc=2, ntf=2, nscm=1000
> ntb=0, igb=5, saltcon=0.150
> cut=999.0, rgbmax=999.0,
> ntpr=1000, ntwx=1000, ntwr=500000,
> numexchg=1000,
>
> But I found out according to *Amber tutorial A7* that there it is mentioned
> to take *irest=0 and nxt=0* which means no restart and no velocity reading
> from .rst file.
>
> So now I am confused whether I made a mistake or is it ok to take irest=1
> and nxt=5?
irest=1 and ntx=5 is fine. That is what I always use. In fact, you
should always use irest=1 and ntx=5 when restarting a REMD simulation in
order to make sure that every replica is assigned the correct
temperature (if you are restarting from an equilibrated structure the
temperatures have not yet been scrambled so irest can be set to 0).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue May 13 2014 - 06:30:03 PDT
