Re: restarting ABF simulation

From: Subramanian Vaitheeswaran (vaithee_at_umd.edu)
Date: Mon Apr 14 2008 - 12:21:43 CDT

Hi Jerome,

This brings up a question about "abf inFiles" I have had for some time. I thought including all the previous output files as Luca proposed for a sequence of restarted runs, is not wrong, merely unnecessary. It would be a big help if you could clarify this point.

thanks,
Vaithee

---- Original message ----
>Date: Mon, 14 Apr 2008 09:54:07 -0400
>From: "Jerome Henin" <jhenin_at_cmm.chem.upenn.edu>
>Subject: Re: namd-l: restarting ABF simulation
>To: "Luca Bellucci" <bellucci14_at_unisi.it>
>Cc: namd-l_at_ks.uiuc.edu
>
>Luca:
>No, you haven't clarified it! But it's not your fault. The manual is
>not clear enough on this question...
>
>When we wrote "This command may also be used to combine data obtained
>from separate runs.", we meant *independent* runs covering *different*
>ranges of the reaction coordinate ("windows"). This does NOT apply to
>a sequence of runs restarted from one another, because all previous
>data provided as input is already carried over in the output.
>
>This means that under normal circumstances, inFiles should really have
>only ONE argument.
>
>Jerome
>
>
>On Mon, Apr 14, 2008 at 9:04 AM, Luca Bellucci <bellucci14_at_unisi.it> wrote:
>> Hi Jerome,
>> I have just read the manual....
>> then to combine multiple abf runs I should to use
>> abf inFiles md01-file.dat md02-file.dat md03-file.dat
>> I hope to have clarified the use of "abf inFiles" command for other user.
>> Anyway thanks for replay.
>> Luca
>>
>>
>>
>> > Luca,
>> > Just restart the NAMD simulation as you would normally do, providing
>> > the same ABF parameters as in the first run, with the "abf inFiles"
>> > parameter pointing to the previous ABF data file containing the free
>> > energy, its gradient and the sampling histogram.
>> > Jerome
>> >
>> > On Mon, Apr 14, 2008 at 5:14 AM, Luca Bellucci <bellucci14_at_unisi.it> wrote:
>> > > Dear all,
>> > > My simulation is prematurely finished (6ns of 10ns),
>> > > How restart ABF simulation?
>> > >
>> > > any suggestions are well accepted
>> > > Luca
>> > >
>> > >
>> >
>>
>>
>

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