Re: restarting ABF simulation

From: Luca Bellucci (bellucci14_at_unisi.it)
Date: Mon Apr 14 2008 - 10:00:21 CDT

Ok.
Well, then I can to use infiles command for
-1- restart abf simulation or extend it in sequential mode
-2- joint different ranges of sequential windows of the reaction coordinates.
thank you

> 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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