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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> >
>
>
>
> --
> ================================ 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
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Received on Wed Sep 14 2011 - 11:00:04 PDT
