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 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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