Ok.
I need to run a short equilibration MD first for all the replicas or just one
and the use this structure for all the replicas??? This little run at what
temperature will be if the lower temperature of the replica is 330k, (ex.
from 0 to 298 for 200ps)???Then I need to set the tempi of all replicas equal
to the temperature of this littler run ???
Anthony
On Tuesday 13 September 2005 5:25 am, Carlos Simmerling wrote:
> Anthony Cruz wrote:
> >Thank you for your answer.
> >I find an error in the *.in files, :
> >I have this irest = 1, ntx = 5, and sander cand find the velocities so
> > I change it to irest = 0, ntx = 1, because I start all the replicas
> > with the same minimized structure.
>
> you need to use irest=1, ntx=5. Amber9 will have more
> extensive checking of REMD inputs. Just run a short equilibration MD first.
> The reason is that after each exchange the input is re-used and
> you need to have all of the data read from the restart file.
> carlos
>
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Received on Tue Sep 13 2005 - 17:53:00 PDT
