RE: Energy Gradient Plotting

From: Radak, Brian K (
Date: Wed Jan 18 2017 - 11:19:04 CST

The energy gradient (negative forces) are not printed to the log file. You can write a binary force file by using the forceDCDfile and forceDCDfreq keywords or else the output command with the "onlyforces" (see p 18 of the user guide, this is a somewhat hidden option).

I have no idea if grace can visualize those files since they are in binary format and I also don't know what exactly you are looking for.

The interpretation of the cell basis vectors depends on your box shape - the easiest (and probably most robust) way to determine these is to run a simulation at constant pressure until the force field chooses an equilibrium volume. Otherwise the burden is strictly on your method for building your system.


Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory

9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
From: [] on behalf of Zeki Zeybek []
Sent: Wednesday, January 18, 2017 2:19 AM
Subject: namd-l: Energy Gradient Plotting

Hello !

I was wondering is there any way to plot the energy gradient with xmgrace using the log file as we do with the energy.dat file. And also another thing is that even though there are a couple of entries about cellbasisvectors none of them explains how we can determine the value of cellbasis vectors. Some say little bigger than the box dimension some say exactly the same.... Thank you for your replies.

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