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?
--
Saikat Dutta Chowdhury
Research Fellow
University of Calcutta
India
Mobile: 8017650842
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Received on Tue May 13 2014 - 05:30:03 PDT
