From: Qasim Pars (qasimpars_at_gmail.com)
Date: Thu Jun 25 2020 - 08:03:45 CDT
I should change only the "runFEP" line at the end of the config file and
the other lines will stay the same, right?
Lastly, will NAMD append to the old output files if I rerun the FEP
simulation? Normally I use "srun namd2 +setcpuaffinity backward.conf >
backward.log" to run a FEP simulation but I think I should change that
command also while reruning the simulation?
It would be good if NAMD appends to the old output files... but don't know
how to do it.
On Thu, 25 Jun 2020 at 15:12, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
> Dear Qasim,
> To restart the simulation, you should find the last lambda value that was
> computed. If it was, for example, 0.7, then the lines at the end of the
> config file would become:
> runFEP 0.7 1.0 0.1 $nSteps
> That is, run from lambda=0.7 to 1, in increments of 0.1.
> And then you continue with the backwards simulation:
> runFEP 1.0 0.0 -0.1 $nSteps
> which may also end up split into several NAMD runs.
> ----- On 25 Juin 20, at 9:37, Qasim Pars qasimpars_at_gmail.com wrote:
> > Dear users,
> > I run a free energy simulation as in this tutorial
> > but my simulation stops due to the time limit of slurm system. Do you
> > I can restart the simulation?
> > It would be good if you write the restarting command.
> > Regards,
> > --
> > Qasim Pars
-- Qasim Pars
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