[gmx-users] How To Calculate The Energy From The Coordinates Of Pdb File?

Braden Kelly bkelly08 at uoguelph.ca
Fri Dec 28 22:28:01 CET 2018

Hello Mehdi,

It seems to me you are after a Single Point Energy Calculation. The fact that you have many means that it will be convenient for you  to make a loop that will do the same thing on each pdb file.

Here is some documentation http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy

Single-Point Energy - Gromacs<http://www.gromacs.org/Documentation/How-tos/Single-Point_Energy>
Computing the energy of a single configuration is an operation that is sometimes useful. The best way to do this with GROMACS is with the mdrun -rerun mechanism, which applies the model physics in the .tpr to the configuration in the trajectory or coordinate file supplied to mdrun.. mdrun -s input.tpr -rerun configuration.pdb

If all of your pdbs are for the same system (i.e., have the same topology), just at different times as the system evolved, you should only need to run grommp once the usual way you would for a simulation to generate your .tpr file. Once you have this all you need to do is

mdrun -s input.tpr -rerun configuration.pdb

here "input.tpr" is the tpr file that grommp generates for you. If your topologies are the same you can keep reusing the input.tpr file for all configurations you have saved. You can then analyze the resulting energy using gmx energy -f ener.edr (or whatever you called the ".edr" file).

I would advise making a bash script that will automatically call the energy after you run mdrun, and store that value. If you do this, then you can create a loop. Each pass you will call mdrun as above, then store the energy in a file, and carry on until all configurations have been read.

But that is your call. Once you use grommp once, you just use the command I gave above, and then the usual gmx energy -f ener.edr command to evaluate energy. and repeat as needed for all your configurations.


From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Mehdi Mirzaie <mirzaie.mhd at gmail.com>
Sent: Friday, December 28, 2018 2:58:29 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] How To Calculate The Energy From The Coordinates Of Pdb File?

Dear Groamcs User,

I am new in using Gromacs.

I would be appreciated if you guide me, how to calculate energy from the
coordinates of PDB file? In fact I have thousands of Pdb files and would
like to calculate energy for each of them using Gromacs. Since the Pdb
files are already minimized, obviously, there is no needed to run energy
minimization step.


*Mehdi Mirzaie(PhD),*

Department of Applied Mathematics,

Faculty of Mathematical Sciences,

Tarbiat Modares University,

Tehran, Iran

Tel?Fax: +98-021-82884727

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