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<P><FONT SIZE=2>Thanks David for your reply. Anybody has got the script for calculating 2nd virial coefficient<BR>
or can you explain a bit more detail?<BR>
<BR>
Hydrophobic moment basically calculated as vector sum of hydrophobicities of amino acids and cross product of that sum with unit vector pointing from the alpha carbon atom of ith residue.(Zangi, et el, Biophysical Journal, 83: 112-124, 2002)<BR>
<BR>
<BR>
With regards.<BR>
<BR>
Abu Naser<BR>
<BR>
School Of Life Sciences<BR>
Heriot-Watt University<BR>
Edinburgh EH14 4AS<BR>
Email: mn2@hw.ac.uk<BR>
Phone: +44(0)1314518265<BR>
Fax : +44(0) 131 451 3009<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
<BR>
-----Original Message-----<BR>
From: gmx-users-bounces@gromacs.org on behalf of David van der Spoel<BR>
Sent: Fri 22/06/2007 8:40 AM<BR>
To: Discussion list for GROMACS users<BR>
Subject: Re: [gmx-users] 2nd Virial coefficient and Hydrophobicmoment Calculation<BR>
<BR>
Naser, Md Abu wrote:<BR>
> Hi GMX user,<BR>
><BR>
> Is there anyway I can calculate 2nd virial coefficient and hydrophobic<BR>
> moment using gromacs?<BR>
> I guess 2nd virial coefficient calculated somewhere in the gromacs.<BR>
><BR>
> Thanking you,<BR>
><BR>
2nd virial: people use scripts that generate different orientations and<BR>
distances and then compute it from there. Alternative would be to do gas<BR>
sims at different T and measure the deviation from the ideal gas law.<BR>
<BR>
hydrophobic moment: don't know. what is that again?<BR>
<BR>
--<BR>
David.<BR>
________________________________________________________________________<BR>
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<BR>
Dept. of Cell and Molecular Biology, Uppsala University.<BR>
Husargatan 3, Box 596, 75124 Uppsala, Sweden<BR>
phone: 46 18 471 4205 fax: 46 18 511 755<BR>
spoel@xray.bmc.uu.se spoel@gromacs.org <A HREF="http://folding.bmc.uu.se">http://folding.bmc.uu.se</A><BR>
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