[gmx-users] how to extract structure from trajectory file

David spoel at xray.bmc.uu.se
Wed Feb 26 06:35:28 CET 2003

On Wed, 2003-02-26 at 02:28, Liu Songbai wrote:
> hi, all 
> I did a free molecular dynamics modeling of a pharmaceutical molecule 
> solvated in water. After finishing the modeling, I want to extract the 
> structure of the molecule to calculate its potential energy and find the 
> structure of lowest engergy. But I am wondering how to do this and if it's 
> necessary to perform 100 step energy minimization after I extract the 
> structure from trajectory file because I plan to compare their potential 
> energy.
If you used two energy groups:
one for your moleucules and one for solvent you can extract the energy
terms directly from the .edr file with g_energy

extract the coordinates of just the molecule you do with
trjconv -f traj -n index -o struct.trr
(see trjconv -h)
> Any suggestions? 
> Songbai Liu 
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell and Molecular Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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