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 systemin 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
--
==
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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