[gmx-users] Contribution of delta bonding energy in the delta free energy

[afsaneh maleki]

Dear Mark,

I used thermodynamics integration method (TI) to obtain delta Gibbs energy
of the protein membrane with dual topology.

topology A (lambda=0) to topology B (lambda=1)
What i obtained after using mdrun command to calculate free energy is
dgdl.xvg that contain dV(total)/dlamda via time. I want to obtein
dV(bond)/dlamda and dV(non-bond)/dlamda, seperetly. dV(bond)/dlambda and
dV(non-bond)/dlambda are not writed in free.edr and free.log. how to produce
dv(bond)/dlambda and dV(non-bond)/dlambda.
my version gromacs is 4.0.5 and 4.0.7.


Thanks in advance,
Maleki

On Tue, Aug 9, 2011 at 6:18 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 9/08/2011 9:13 PM, afsaneh maleki wrote:
>
> Hi,
>
>
>
> I used thermodynamics integration method (TI) to obtain delta Gibbs energy
> of the protein membrane. I want to separate contributions of delta bonding
> and nonbonding energy in delta Gibbs energy.
>
>
> So instead of using the sum of bonded and non-bonded energy (i.e. total
> PE), use them separately. Whether that will mean anything is up to you to
> demonstrate.
>
> Mark
>
>
>
> Best wishes,
>
> Maleki,
>
>
>
>
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