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
and/or charges)?
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.
-Justin
Thanks in advance,
Maleki
On Tue, Aug 9, 2011 at 6:18 AM, Mark Abraham <[email protected]
<mailto:[email protected]>> 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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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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