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

Abhishek Acharya abhi117acharya at gmail.com
Sun Sep 10 04:32:38 CEST 2017

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.

Okey, one thing that I presumed while performing the second transformation
is that it is sufficient to 'turn-off' charge electrostatics just by
stating c-lambda0=none and c-lambda1 = vdw (or vice-versa). It doesn't
matter if the topology files have the charges or not. Therefore, i had
included the charges in my topology file.

Then this explains the problem in my case. Thank you so much Wes for
clarifying that out.

Abhishek Acharya

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