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

[Liu Songbai]

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. 
Any suggestions? 
Songbai Liu 





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