[gmx-users] Re: freeenergy calculation

Liang petrucci86 at vip.sina.com
Fri Jun 2 02:09:10 CEST 2006

Date: Thu, 01 Jun 2006 15:34:14 +0530
From: "lalitha selvam" <hayagrivar at hotmail.com>
Subject: [gmx-users] freeenergy calculation
To: gmx-users at gromacs.org
Message-ID: <BAY115-F83B8E1F1CB3FAA8254937C7900 at phx.gbl>
Content-Type: text/plain; format=flowed

i have completed my simulation.i want to analyse my protein.can u help me
how to calculate the free binding energy calculation,which program i should
use.i've read gromacs manual 3.3 but i'm in need of any other new analysis
are included in version 3.3 or not.so where can i getthe information on
availability of more analysis in GROMACS 3.3 version comapred to older
thanks sir.i'm in hurry.Plz anyone help me.

hello, you can use g_sham program (new one in 3.3)to calculate free energy
distribution and draw the picture.
first, you should prepare a xvg file with three columns. the first is frame
time, the second and third are the parameters you want to calculate, for
example like this:

Time     RMSD     dist
0             1.2          0.8
1             1.3          1.1
2             0.5          0.9
.               .             .
.               .             .

and then, use the following command:

g_sham -f  *.xvg -ls

you can get the pic, and with -ngrid you can get the high resolution pics.

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