[gmx-users] Contribution of delta bonding energy in the delta free energy
Justin A. Lemkul
jalemkul at vt.edu
Wed Aug 10 01:32:47 CEST 2011
afsaneh maleki wrote:
> 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 did you alter between these two topologies? Nonbonded terms (atom types
> 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.
If you simply removed/added charges and/or van der Waals terms, then
dV(bonded)/dlambda = 0 since the bonds are unaffected. If you are looking to
completely remove all bonded and nonbonded terms from a given molecule, you will
have to do extensive topology modifications to eliminate bonds, but in that case
your molecule will just fly apart (as a function of lambda) and give a
meaningless result. You can mutate molecules (e.g. FEP of molecule A to B), but
completely turning off all intra- and inter-molecular interactions using TI does
not lend well to obtaining the information you seek.
> Thanks in advance,
> On Tue, Aug 9, 2011 at 6:18 AM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
> On 9/08/2011 9:13 PM, afsaneh maleki wrote:
>> 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.
>> Best wishes,
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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