From: Chitrak Gupta (chgupta_at_mix.wvu.edu)
Date: Wed Oct 11 2017 - 14:32:54 CDT
I have not done FEP but have used the REST2 version you referred to. Could
you elaborate why you mean by "well-behaved" and what problem you had in
your case 2?
On Wed, Oct 11, 2017 at 3:12 PM, Bhati, Agastya <agastya.bhati.14_at_ucl.ac.uk>
> I have been performing FEP/REST2 simulations using the customised NAMD
> developed by Sunhwan and Wei (https://doi.org/10.1016/j.cpc.2015.08.030
> I observed that sortreplicas executable seems to do correct sorting only
> when the trajectory files contain one extra snapshot. Let me elaborate this
> point with the following example cases.
> - Case 1 (Fresh run): I set "steps_per_run", "runs_per_frame" and
> "num_runs" variables as 500, 10 and 4000, respectively. In addition, I run
> a 5000 step equilibration before attempting the first exchange. Therefore,
> the output trajectories have 401 snapshots. In this case, "sortreplicas"
> seems to sort the trajectories correctly with the final sorted trajectories
> containing only 400 snapshots. I am not sure what happens to the extra
> snapshot here but the sorted trajectories are well-behaved.
> - Case 2 (Restarted run): I use the same input parameters as mentioned in
> case 1 above for a restarted simulation. Since in this case no
> equilibration is done before exchanging begins, the number of snapshots is
> 400. In this case, the sorted trajectories, which contain 400 snapshots, do
> not behave correctly and have problematic conformations.
> - Case 3: I added the last snapshot of the unsorted trajectories from case
> 1 to the beginning of the unsorted trajectories from case 2. These modified
> trajectories contain 401 snapshots. On sorting these modified
> trajectories using sortreplicas, the resultant trajectories have 400
> snapshots and are well-behaved.
> My conclusion from the above three cases is that sortreplicas appears to
> do what is desired only when there is an extra snapshot at the beginning of
> the unsorted trajectories. I am not sure why does this happen and how
> sortreplicas gets rid of the extra snapshot. Does anyone else experience
> similar thing and understand it or am I missing something here and doing
> something wrong? If my conclusion is correct, is there a special way of
> implementing sortreplicas executable for restarted simulations where no
> extra snapshot is present?
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