Well if you don't know what the 2nd column is, how do you expect to produce
such a file with AMBER? The workings of GROMACS are entirely foreign to me
(no pun intended) and I have no idea what their inputs or outputs are
supposed to look like. I would not at all be surprised if they are entirely
different than anything produced by AMBER.
What MBAR code are you using? I use a locally modified version of the
Pymbar code distributed by Shirts and Chodera from a few years ago (2009 I
believe?), which is the only such code that I know of (not that I have
looked very hard) and it includes no such general utility for PMF
calculations. If possible you should look at the MBAR code and discover
what exactly it is doing so that you can devise the proper input data.
Regards,
Brian
On Wed, Sep 14, 2011 at 2:36 PM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> Dear Brian and experts in MBAR,
>
> In the example file comes with the MBAR. I can see the following headings
> which was created by the following command in GROMACS. This is one of the
> input file needed to be submitted for MBAR runs. I guess the 3rd column is
> the potential energy, the first column is time. But the 2nd column is
> unknown to me. I am wondering how to generate this file with AMBER, ptraj
> or others.
>
> Could you mind to give me some help?
>
> Commands: g_energy -f prod0.ene -o analysis/prod0_energies.xvg
>
> Part of the input file:
>
> . title "Gromacs Energies"
> . xaxis label "Time (ps)"
> . yaxis label "E (kJ mol\S-1\N)"
> .TYPE xy
> . view 0.15, 0.15, 0.75, 0.85
> . legend on
> . legend box on
> . legend loctype view
> . legend 0.78, 0.8
> . legend length 2
> . s0 legend "Dih. Rest."
> . s1 legend "Potential"
> 0.000000 2.055618 -277697.093750
> 0.200000 0.012398 -277960.375000
> 0.400000 0.549604 -277840.437500
>
>
>
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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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address.
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Received on Wed Sep 14 2011 - 13:00:02 PDT
