Re: [AMBER] Extract potential energy from ptraj?

From: Adrian Roitberg <roitberg.qtp.ufl.edu>
Date: Tue, 09 Mar 2010 23:18:04 -0500

Hi Lili.
There is no way to extract it from the mdcrd directly, or through ptraj.

However, look in the sander manual at the imin=5 option. It will read
the mdcrd/prmtop and compute single point energies for each snapshot,
which will give you the potential energy.

Adrian


On 3/9/10 11:05 PM, Lili Peng wrote:
>>
>> Dear AMBER users,
>>
>> I'd like to know if it is possible to extract potential energy information
>> from *.mdcrd files using the ptraj module? After perusing multiple
>> websites, I know the potential energy is provided in the output files
>> (*.out) from a simulation. The issue is if the PE can also be extracted
>> from *.mdcrd files.
>>
>> Thanks,
>> Lili
>>
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-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry
                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society
University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian.qtp.ufl.edu
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Received on Tue Mar 09 2010 - 20:30:04 PST
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