From: Shyno Mathew (sm3334_at_columbia.edu)
Date: Sat Mar 22 2014 - 14:00:06 CDT
I am trying to combine 3 different .fepout files.
As I metioned in the previous posts, my run was terminated during the
lambda window 0.58 to 0.5825.
850/10,000 equilibration steps were completed. The restart frequency is
So did a restart for the lambda window 0.58 to 0.5825 for only 9200
equilibration steps, followed by 20,000 production steps.
Then I did another run for the remaining windows lambda= 0.5825 to 1
So I have three .fepout files to combine so I can do further analysis with
I was wondering if there is an easy way to combine these files, or should I
write a code to do this?
any help will be appreciated.
On Mon, Mar 10, 2014 at 12:58 PM, Shyno Mathew <sm3334_at_columbia.edu> wrote:
> there are slight modifications to the questions I posted.
> This run was terminated during the lambda window 0.58 to 0.5825.
> 850/10,000 equilibration steps were completed. The restart frequency is
> So this means I should first do a restart for the lambda window 0.58 to
> 0.5825. I need to do only 9200 equilibration steps, followed by 20,000
> This run was terminated during the lambda window 0.43 to 0.425.
> All the 10,000 equilibration steps were completed. The restart frequency
> is 100fs.
> 17,780/20,000 productions steps were completed.
> So this means I should first do a restart for the lambda window 0.43 to
> 0.425. I need to do only 2300 production steps as the equilibration is
> Can some one confirm this?
> On Wed, Mar 5, 2014 at 1:43 PM, Shyno Mathew <sm3334_at_columbia.edu> wrote:
>> Dear all,
>> We had to shutdown our cluster recently and this terminated all the FEP
>> runs. I haven't restarted an FEP before.
>> For each window, I have 10,000 equilibration steps followed by 20,000
>> production steps.My system was crashed for the lambda window 0.58 to
>> 0.5825. From the .fepout file, it looks like only 850/10000 equilibration
>> steps were done.
>> Looking at the previous post, this is what I think I should do:
>> 1. Run FEP for the window where it was crashed, here 0.58 to 0.5825
>> My restart frequency is 1000 fs. Since it crashed at 850, I assume I can
>> do the whole equilibration.
>> But I have other systems which crashed at 1050 fs, here I only do part of
>> the equilibration?
>> 2. Then use the restart files to run the remaining FEP, 0.5825 to 1 and
>> manually combine the .fepout files.
>> Shyno Mathew
>> PhD student
>> Department of Chemical Engineering
>> Columbia University
> Shyno Mathew
> PhD student
> Department of Chemical Engineering
> Columbia University
-- Shyno Mathew PhD student Department of Chemical Engineering Columbia University
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