Knowledge Base

Article ID: 295 - Last Modified:

I want to run the script manually to perform analysis on a subset of frames. How can I do that?

To run the script manually, you will need to locate, collect, and rename a few files. First, you will need to find the .dE files from the production run trajectory, which should be stage 11. That is, you need to unpack the following .tgz file:


Inside, you will need to locate the .dE files, which are named according this scheme:


Copy all of these files into a new directory, and rename the files according to this scheme:


You can then run using a command like the following:

$SCHRODINGER/run -FROM desmond -b 150.0 -e 600.0 -F 2 -R 1 -T 298.15 -s gibbs.%d.dE -l 0 -L 11 -o 150_600.result

This will instruct to estimate the dG values for the time range from 150 to 600 ps. The flag -F and -R correspond to the forward (-F) and reverse (-R) mutations.

The command assumes that there are 12 lambda windows labeled from 0 to 11.

Keywords: Desmond, MD analysis, bennett

Back to Search Results

Was this information helpful?

What can we do to improve this information?

To ask a question or get help, please submit a support ticket or email us at
Knowledge Base Search

Type the words or phrases on which you would like to search, or click here to view a list of all
Knowledge Base articles