[gmx-users] GBSA calculations

Mark Abraham mark.abraham at anu.edu.au
Sun Jul 4 13:31:33 CEST 2010

----- Original Message -----
From: Hassan Shallal <hshallal at PACIFIC.EDU>
Date: Friday, July 2, 2010 17:40
Subject: [gmx-users] GBSA calculations
To: gmx-users at gromacs.org

  <!-- .hmmessage P { margin:0px; padding:0px } body.hmmessage { font-size: 10pt; font-family:Verdana } -->  -----------------------------------------------------------

 > Dear Gromacs users,   >   > I am running some simulations of ligand protein systems using GBSA option for the implicit solvent. > In an MM/GBSA model, there is this equation: >   > G(molecule) = G(solvations) + Egas - TS(solute)... > G(molecule) is the total free energy of solute > G(solvations) is the solvation free energy > Egas is the moelcular mechanical energy of the molecule summing up the electrostatic interactions, van der Waal contributions and the internal strain energy > TS(solute) is the sum of TS(trans), TS(rot), and TS(vib) >   > How can derive such a calculation from the input of my Gromacs simulation... > I looked in the mailing list, there were a couple of inquiries about this issues without reponses. > I know those calculations can be run through Amber which I don't have an access to, so first question is, can I execute those calculations from the Gromacs simulation output files like from the .edr for example? and if yes, any hint or reference on how to do this would be greatly appreciated...

Until the release of GROMACS 4.5, this will not be available. After that release, it will surely be in the manual :-)


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100704/24c4b786/attachment.html>

More information about the gromacs.org_gmx-users mailing list