[gmx-users] Free Energy Calculations: Error during minimization step.

Wes Barnett w.barnett at columbia.edu
Sat Sep 9 20:40:22 CEST 2017

On Sat, Sep 9, 2017 at 10:10 AM, Abhishek Acharya <abhi117acharya at gmail.com>

> Hello Wes,
> 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

You can do them separately, but the charges need to have been turned off
for the molecule you are transforming for the second step when turning off
vdw. In other words, all charges must be 0.0 for the molecule in the
topology file for the vdw transformation. Is that what you've done?

Justin's tutorial gives an explanation on why this needs to be done, and in
his topology he had all charges at 0.0 in the methane topology file.

James "Wes" Barnett
Postdoctoral Research Scientist
Department of Chemical Engineering
Kumar Research Group <http://www.columbia.edu/cu/kumargroup/>
Columbia University
w.barnett at columbia.edu

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