How to compute "only the GB Energy" using NAMD?

From: jesmin jahan (
Date: Mon Dec 03 2012 - 20:34:02 CST

Dear NAMD users,

I am new to NAMD.

I am comparing performance of several MD packages (for example Amber,
Gromacs &NAMD) wrt to the computation of GB energy. For this, I need
to know the GB energy value along with the time to compute the
GB-energy value for NAMD.

I wanted to know whether there is a way to compute the GB energy
without calculating any other kind of energy terms.

By this I mean to turn off all bonded energy and VWD energy terms.
Also, I do not want to compute the GB forces, I only want the energy

So far, what I have done is to run single point simulation by first
turning the GBIS off and then GBIS on. Then I am taking the difference
in the Electrostatic energy value from these two simulations to get
the GB energy value.

To get the running time, I am taking the difference of GBIS on-GBIS off run.

Now, my question is, Is there any better way to do this?

If anyone can help me with this, that will be really appreciable.

Thanks in advance,

Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.

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