AMBER Archive (2007)

Subject: Re: AMBER: How to extract energy of molecule from the system with explicit water molecules

From: priya priya (priyaanand_27_at_yahoo.co.in)
Date: Thu Jul 05 2007 - 10:10:23 CDT

Hi,
i want to extract the potential energy of the peptide without including the water molecules and not including the interaction of peptide with water.
I want it to calculate all the frames of the trajectory,
Regards
priya

Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote: do you mean just the internal energy, or also the interaction with
water? the latter is difficult in a periodic system. if you want just
the peptide energy, you can use ptraj to strip the water and then
make a prmtop of just the peptide without water. then you can
evaluate the energy of the peptide. if you want more specific suggestions
you'll need to make clear what you want- energy for a restart
file, or for all frames in the trajectory, energy with or without peptide:water
interaction, and so on.

On 7/5/07, priya priya <priyaanand_27_at_yahoo.co.in> wrote: Dear All

I am interested in extracting the energy of the molecule i.e peptide only from the output file that i obtained from running MD of that peptode in explicit solvent (water).

Please suggest me something!
Regards
 

                         
---------------------------------
 Here’s a new way to find what you're looking for - Yahoo! Answers
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu