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: [EMAIL PROTECTED]
Phone: +44(0)1314518265 
Fax : +44(0) 131 451 3009 


 



-----Original Message-----
From: [EMAIL PROTECTED] 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.
________________________________________________________________________
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
[EMAIL PROTECTED]       [EMAIL PROTECTED]   http://folding.bmc.uu.se
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