[gmx-users] About free enrgy calculation

Justin Lemkul jalemkul at vt.edu
Sun Jun 1 19:57:47 CEST 2014

On 6/1/14, 3:30 AM, vidhya sankar wrote:
> Thank you for your previous reply
> Sorry  In previous Mail i wrongly  stated that decoupling CNT ( as you stated  it is big  Molecule )
> To do free energy calculation based on on your tutorial 6( methane/water)
> I  want to decouple  Water  from CNT which is Wrapped by  assembly of Cyclic peptide  (the stability of assembly is mainly due to Vandewall's interaction between CNT and cyclic peptide)

Decoupling water from the system will likely be highly unstable and I'm not sure 
what use the value is, if the simulations even run.

> When  I  Fix  following  parameter for My system    in mdp files
> free_energy              = yes
> init-lambda         = 0.00
> delta_lambda             = 0.00
> sc-alpha                 = 1
> sc-power                 = 2.0

The values of sc-alpha and sc-power are unusual.  I stick by my recommendation 
to use the same settings as in my tutorial.

> sc-sigma                 = 0.3
> It show follwin Notes How to Avoid this?
> NOTE 1 [file /usr/local/gromacs4.6.11single/bin/MDP/em_steep_0.mdp]:
>    With PME there is a minor soft core effect present at the cut-off,
>    proportional to (LJsigma/rcoulomb)^6. This could have a minor effect on
>    energy conservation, but usually other effects dominate. With a common
>    sigma value of 0.34 nm the fraction of the particle-particle potential at
>    the cut-off at lambda=0.5 is around 2.4e-04, while ewald-rtol is 1.0e-05.
> May i extend your tutorial parameter  to my system ? because you also Decouple water from Metahne . Or is ther is Any Thump rule

No, I don't decouple water from methane, I do the opposite.  The water 
interactions remain the same at all lambda values.  The methane molecule is 
decoupled to calculate the free energy of hydration.  I don't get a clear sense 
of what you're even trying to calculate in your system.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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