Both cases of what? PMF is an observable (of sorts), not a simulation
protocol, which is what REMD is.
I am not sure what file you are referring to. Is this a file from AMBER or
a file format for a program that implements MBAR? Very much guessing, but I
would suspect that the 2nd column is the value of the reaction coordinate
when the energy was evaluated. This is of course needed if you are
calculating the PMF as it requires you to estimate the marginal density of
the reaction coordinate.
Brian
On Wed, Sep 14, 2011 at 1:50 PM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> Dear Brian,
>
> I am doing both cases, PMF and REMD.
>
> I found when we do PMF, I can see there are three columns in MBAR, energy
> file. The first is time, the second is ???, the third one is energy.
>
> Could you mind to let me know what is the entries in the 2nd column? Is
> the 3rd column same as the potential energies listed in the output files?
>
> Best regards,
>
> Catherine.
>
>
> > Date: Wed, 14 Sep 2011 10:01:18 -0400
> > From: radak004.umn.edu
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] How to extract time angle, time, Energy from for
> MBAR analysis?
> >
> > Catherine,
> >
> > I believe this depends on how your simulations were run and which module
> you
> > used.
> >
> > If you are doing umbrella sampling:
> > Both the ncsu and nmropt modules produce time series files similar to the
> > first type you describe. You would probably have to write a simple script
> > to produce the second file, assuming you used a simple analytic biasing
> > potential (e.g. harmonic).
> >
> > If you are doing something else (e.g. REMD):
> > You would have to calculate the order parameter of interest using ptraj
> or
> > some other analysis program (I'm personally more used to VMD). As for the
> > energy, it would probably have to be recalculated from your trajectory.
> > I've never actually done this personally, but I believe there is an
> > established AMBER protocol for it (check the manual, this may also only
> be
> > in very recent AMBER releases).
> >
> > Hope that answers your question,
> > Brian
> >
> >
> > On Wed, Sep 14, 2011 at 9:37 AM, Catein Catherine <
> askamber23.hotmail.com>wrote:
> >
> > >
> > > Dear All,
> > > I am trying to use MBAR to calculate the PMF energy profile.
> > > I found in order to run MBAR, we need to input two columns.
> > > One file contains:. xaxis label "Time (ps)"
> > > . yaxis label "Angle (degrees)"
> > >
> > > Another file contains:. xaxis label "Time (ps)".
> > > yaxis label "E (kJ
> > > mol\S-1\N)"
> > >
> > > Could you mind to let me know how can we use AMBER to generate those
> input
> > > files for MBAR analysis?
> > > Best regards,
> > > Catherine
> > > _______________________________________________
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> > > AMBER.ambermd.org
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> > >
> >
> >
> >
> > --
> > ================================ Current Address =======================
> > Brian Radak : BioMaPS
> > Institute for Quantitative Biology
> > PhD candidate - York Research Group : Rutgers, The State
> > University of New Jersey
> > University of Minnesota - Twin Cities : Wright-Rieman Hall 101
> > Graduate Program in Chemical Physics : 610 Taylor Road,
> > Department of Chemistry : Piscataway, NJ
> > 08854-8066
> > radak004.umn.edu :
> > radakb.biomaps.rutgers.edu
> > ====================================================================
> > Sorry for the multiple e-mail addresses, just use the institute
> appropriate
> > address.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
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>
> _______________________________________________
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Wright-Rieman Hall 101
Graduate Program in Chemical Physics : 610 Taylor Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Wed Sep 14 2011 - 11:30:04 PDT
