Date: Wed Jul 22 2015 - 03:10:42 CDT
Free energy of solvation is the dG associated with the transfer of a molecule into a solution. You actually want to simulate the opposite direction so you need to decouple solute and solvent from each other. The end-points describe a solvent with a filled void and the molecule in gas phase. The crucial point is that the molecule in gas phase has to be properly described with both bonded and intra non-bonded terms. To have the latter not scaled with lambda you can set alchDecouple to on (see User's Guide). You can also set it to off and explicilty calculate the free energy of switching off the intra non-bonded terms for correction. I think this is basically a technical issue and older codes of NAMD (the email response you cite is over ten years old) may not have had this feature.
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Mohan maruthi sena [maruthi.sena_at_gmail.com]
Sent: 22 July 2015 08:25
Subject: namd-l: FEP method- Free energy of solvation of ligand
I want to calculate free energy of solvation for a ligand in water using FEP method in NAMD. I read the following post in mailing list,
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2003-2004/0186.html, in which free energy solvation of methyl alchol is calculated as shown below,
Asolv(MeOH) = A*(MeOH, vacuum) - A*(MeOH, water)
where Asolv solvation free energy
A* be the free energy of anihilation.
My question is as follows,
Is it not enough if we calculate the MeoH+water ------ dummy+water.
Doesn't this corresponds to free energy of solvation of MeOH?
Thanks & Regards,
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