On 9/16/12 10:45 PM, Sonia Milena Aguilera Segura wrote:
Hi,
I'm preparing my mdp and topology files for running free energy calculations
using BAR method. I´m using Justin Lemkul's tutorial as a reference (You can
find it here
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/08_advanced.html).
According to this tutorial, the simultaneous coupling of both Coulombic and
van der Waals terms leads to instability. So, it is usefull to prepare the mdp
files as follows (off course including all other parameters):
van der Waals coupling:
sc-alpha = 0.5 ; use soft-core for LJ (de)coupling
sc-sigma = 0.3
sc-power = 1
couple-moltype= LIG
couple-intramol = no
couple-lambda0= none; non-interacting dummy in state A
couple-lambda1= vdw ; only vdW terms on in state B
Coulombic coupling:
sc-alpha = 0 ; soft-core during (dis)charging can be
unstable!
sc-sigma = 0
couple-moltype= LIG
couple-intramol = no
couple-lambda0= vdw ; only vdW terms in state A (the previous
state B is now A)
couple-lambda1= vdw-q ; all nonbonded interactions are on in state B
However, I don't understand how can this leads to a fully interacting molecule
if all the charges in the topology file have been set to zero. Does it mean
that for the second calculation (coulombic coupling) I have to use the original
topology file with all charges? Or, should I use the same topology with zero
charges?
You do not need to make any changes to the topology. The couple-lambda*
settings dictate which parameters are involved in the calculations. In the
second examples, in the lambda=0 state, only van der Waals interactions are
calculated, but when lambda=1, both van der Waals and Coulombic interactions
(vdw-q) are calculated.
-Justin
--
Justin A. Lemkul, Ph.D.
Research Scientist
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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