Hello,
ptraj cannot do this. You can write a nab program that will do this if you
want. You can also use sander with imin=5, and just take the VDW energies.
This is easily automated with an awk script (or with a simple perl or
python script). There's no utility that will take a trajectory and *just*
dump van der waals energies (unless you write it yourself).
Hope this helps,
Jason
On Wed, Mar 23, 2011 at 5:41 PM, Yuan Ding <uscchem.gmail.com> wrote:
> Hi Amber users,
> I'm new to Amber, and I have a question about energy extraction. Is there a
> way to extract only the vdw energy of a structure and print it out in a
> separate text file by ptraj? I realized the output file of minimization
> includes a list of all kinds of energy, but since I have a lot of
> structures
> to look at, I can't check the vdw energy one by one. If ptraj can't do it,
> can other tools of Amber serve the same purpose?
> Thank you in advance for the help!
> Yuan
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Mar 23 2011 - 19:00:02 PDT
