[gmx-users] Free Energy Calculations: Error during minimization step.
abhi117acharya at gmail.com
Sat Sep 9 16:10:19 CEST 2017
Thanks for your reply.
Sorry, I did not understand why we need to turn off charges first and then
vdw, if the are performing both steps separately.
I was attempting to perform the vdw and charge transformations separately.
So for the vdw transformation, if I use c-lambda0=vdw
and c-lambda1=none, I think that would signal gromacs that the
electrostatics are turned off at all lambda values.and the vdw interpolate
from full strength at lambda=0 to none at lambda=1.0
This is similar to what is done in Justin's free energy tutorial, that you
have provide the link to.
Has the charge been turned off for this series of simulations? You should
generally turn electrostatics off through a series of free energy
simulations and then turn off VDW while the charge is off.
For the charge annihilation transformation. I used couple-lambda0=vdw-q and
I presume that in this case the vdw interactions are never turned off,
while the charges interpolate from full strength at lambda=0 to none at
Kindly correct me if there some mistake in my understanding.
> Looking for the some advice on how to proceed from here.
I do something like this:
vdw-lambdas = 0.00 0.00 0.00 0.00 0.00 0.10 0.20 0.30 0.40
0.50 0.60 0.70 0.80 0.90 1.00
coul-lambdas = 0.00 0.25 0.50 0.75 1.00 1.00 1.00 1.00 1.00
1.00 1.00 1.00 1.00 1.00 1.00
couple-lambda0 = vdw-q
couple-lambda1 = none
Yes I have seen this..I thought the only utility this has is that both vdw
and charge transformations can be done in one shot.
I was planning to run this way, but after the aforesaid (separate)
calculations run correctly.
But, I still don't understand the reason for the above issue in vdw
transformation step. Any clarification will be very helpful.
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