Re: restarting ABF simulation

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Mon Apr 14 2008 - 13:58:57 CDT

Vaithee,
It would actually be somewhat wrong, because in effect the data from
early runs would be duplicated and get an excessive statistical
weight. I am saying "somewhat" wrong because in theory, if you have
independent chunks of data sampled according to the canonical (or NPT)
ensemble, the reweighted average still obeys the right distribution.
In practice, though, it amounts to discarding some information from
the later runs.
Jerome

On Mon, Apr 14, 2008 at 1:21 PM, Subramanian Vaitheeswaran
<vaithee_at_umd.edu> wrote:
> 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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