Anirban Ghosh wrote:
Hello Justin,
Thanks a lot for the reply.
Yes, I am using GROAMCS 4.5 and my system consists of two chains of two
proteins, a substrate and an inhibitor solvated in water. So can you
please tell me what should be the values for:
couple-moltype
The name of the moleculetype you want to decouple. Presumably your ligand.
couple-lambda0
...and couple-lambda1, right? These settings will depend on which part of the
nonbonded interactions (van der Waals and Coulombic interactions) you're
decoupling. Check out the free energy tutorial linked on the Gromacs site for
the underlying theory of what to do, even if the settings have changed somewhat.
The type of interaction you're decoupling will also dictate whether or not you
should use soft-core.
couple-intramol
If you're looking for an absolute binding energy, then set this to "no."
-Justin
Thanks a lot again.
Regards,
Anirban
On Sat, Nov 27, 2010 at 9:15 AM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Anirban Ghosh wrote:
Hi ALL,
I am trying to run free energy calculation and for that in the
md.mdp file I am keeping the following option:
; Free energy control stuff
free_energy = yes
init_lambda = 0.0
delta_lambda = 0
sc_alpha =0.5
sc-power =1.0
sc-sigma = 0.3
But still I find that in my log file the values for
dVpot/dlambda is always coming to be zero.
What I am doing wrong?
Any suggestion is welcome. Thanks a lot in advance.
You haven't indicated your Gromacs version, but assuming you're
using something in the 4.x series, you're not specifying the
necessary parameters to do any sort of transformation, particularly
couple_lambda0 and couple_lambda1. If left at their default values
(vdw-q), nothing gets decoupled.
-Justin
Regards,
Anirban
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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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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