[gmx-users] 2nd Virial coefficient and Hydrophobicmoment Calculation

Naser, Md Abu mn2 at hw.ac.uk
Fri Jun 22 21:27:04 CEST 2007

Thanks David for your reply. Anybody has got the script for calculating 2nd virial coefficient 
or can you explain a bit more detail?

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)

With regards.

Abu Naser 

School Of Life Sciences 
Heriot-Watt University 
Edinburgh EH14 4AS 
Email: mn2 at hw.ac.uk
Phone: +44(0)1314518265 
Fax : +44(0) 131 451 3009 


-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of David van der Spoel
Sent: Fri 22/06/2007 8:40 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] 2nd Virial coefficient and Hydrophobicmoment	Calculation
Naser, Md Abu wrote:
> Hi GMX user,
> Is there anyway I can calculate 2nd virial coefficient and hydrophobic 
> moment using gromacs?
> I guess 2nd virial coefficient calculated somewhere in the gromacs.
> Thanking you,
2nd virial: people use scripts that generate different orientations and 
distances and then compute it from there. Alternative would be to do gas 
sims at different T and measure the deviation from the ideal gas law.

hydrophobic moment: don't know. what is that again?

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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