[gmx-users] The solvation free energy of a vdw ligand

Tanping Li jia_11_osu at yahoo.com
Fri Feb 17 16:07:47 CET 2012

Dear all,

I posted the message yesterday and haven't get a response. My trouble is that: when I calculate the solvation free energy of a vdw ligand, the energy of lambda=0 varies with different state B. 
Does anyone has the similar experience? I greatly appreciate your help since I tried a lot but haven't find the reason.


--- On Thu, 2/16/12, Tanping Li <jia_11_osu at yahoo.com> wrote:

> From: Tanping Li <jia_11_osu at yahoo.com>
> Subject: [gmx-users] The free energy of vdw part
> To: gmx-users at gromacs.org
> Date: Thursday, February 16, 2012, 11:28 AM
> Dear gmx users,
> I am calculating the free energy of solvating a small ligand
> by water, using FEP method. The free energy is separated
> into the contribution of electric+vdw. I find problem for
> the vdw part.
> I am using gromacs-3.3.1. In the top file, I set the state B
> of ligand where LJ parameters of atoms are zero; in the mdp
> file, I set the lamda=0.
> According to my understanding, above setting should gives me
> the energy of ligand's state A. However, when I calculate
> the energy with a mdp with "free_energy=No" and a top
> without setting the B state, I get a very different energy.
> I tried but haven't dig out which part I missed. I greatly
> appreciate your help and consideration on this issue.
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