From: jesmin jahan (shraban03_at_gmail.com)
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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