Re: vmd-l: Fwd: ParseFEP for restating FEP

From: Brian Radak (brian.radak_at_gmail.com)
Date: Fri Mar 23 2018 - 10:48:17 CDT

Unfortunately there is not currently an elegant solution for this. You can
indeed, under certain circumstances, just concatenate output from multiple
runs, but things must be in the right format for ParseFEP to detect it.
That means you would have to sort and interleave the data at the same
lambda value, probably strip out some of the comments, and then
re-concatenate everything into a single file.

If you are running each lambda as its own NAMD job, then this should not be
too hard - just "grep -v #" the fepout files after the first one:

Here's a bash example for N jobs (N-1 restarts) and M lambda values -- I've
assumed a specific file naming scheme that should be pretty transparent and
mappable onto whatever you've done.

rm -f all_lambda.fepout 2> /dev/null
for ((m=0; m<$M; m++))
do
  cat lambda${m}_job1.fepout >> all_lambda.fepout
  for ((n=2; n<=$N; n++))
  do
    grep -v "#" lambda${m}_job${n} >> all_lambda.fepout
  done
done

all_lambda.fepout *should* work in ParseFEP, but I've never actually tried
something like this.

I know this is not pretty and we're trying to improve things for NAMD 2.13,
especially with regards to automating parallel runs.

Brian

On Fri, Mar 23, 2018 at 10:00 AM, Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> Otherwise, is it possible to run portions of lambda and then concatenate
> the .fepout results?
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Fri, Mar 23, 2018 at 8:05 AM
> Subject: ParseFEP for restating FEP
> To: NAMD <namd-l_at_ks.uiuc.edu>, VMD Mailing List <vmd-l_at_ks.uiuc.edu>
>
>
> Hello:
> May I ask whether there is any plan to make ParseFEP plugin capable of
> dealing with restarted FEP.
>
> With receptor-ligand, I found it difficult to get matching free energy for
> frwd/back in the 24hr hr allowed on the cluster, taking into account that I
> used the max number of nodes for the given size of the system.
>
> Thus, for the UNBOUND simulations, with either SOS or BAR estimator,
> Probability Distribution was found to improve from 1 to 4 until good
> overlapping, while Free Energy also improves correspondingly, albeit not
> doing better than red at -2.50, black at -10.0. By restarting until 100
> windows, probably I should have acceptable convergence. Curiously
> Enthalpy/Entropy match better (artifact).
>
> I used fifty windows with 50,000 pre-equilibration and 300,000 FEP only (1
> node), in order to stay within the 24hr. (a smaller number of windows, even
> with much pre-equilibration and FEP, perform worser).
> With the ligand-protein I could use a max of 4 nodes (beyond which no
> higher speed) with perhaps a max of 10 windows. Bad prospects for
> convergence.
>
> Thanks for your attention
>
> francesco pietra
>
>

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