[gmx-users] analysis pdb file

Dallas Warren Dallas.Warren at monash.edu
Mon Feb 27 23:32:17 CET 2012

The trajectory file contains that information (.xtc or .trr).

You can do a couple of things here:
# load the trajectory using your viewer (be careful if the trajectory is large, you may want to change the number of frames it contains using trjconv)
# extract the coordination files (.gro or .pdb) from the trajectory file using trjconv for the appropriate times interested in.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
When the only tool you own is a hammer, every problem begins to resemble a nail.

From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Nathalia Garces
Sent: Tuesday, 28 February 2012 9:24 AM
To: gmx-users
Subject: [gmx-users] analysis pdb file

Good Day,
I ran a molecular dynamic simulation for over a month and I gathered the ".pdb" file containing the molecular structure at the end of the simulation. I can see the final configuration using a pdb viewer but I would like to know if it is possible (without redoing the simulation) to obtain previous configurations of the atoms.

Thank you for your help,

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