Hello,
I am running GAMD and had a question regarding restarting the simulation before the GAMD production run. After equilibration, you need to run a cMD production followed by a GAMD equilibration step.
I am assuming that this step will have irest=1 and ntx=5 since we are continuing from the standard equilibration. However when reading the tutorial on the Miao website (
https://www.med.unc.edu/pharm/miaolab/resources/gamd/tutorial/), it has this step as irest=0 and ntx=1. Question 1: should my cMD/GAMD equil step after my standard equilibration have an irest=0/ntx=1?
Additionally, after running the cMD and GAMD equilibration step, the website has the GAMD production as irest=0 and ntx=1 again. Question 2: Should we be restarting the simulation (irest=0 and ntx=1) or continuing it from the GAMD equilibration (irest=1, ntx=5)?
Sincerely,
Peter Ramdhan
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Received on Tue May 14 2024 - 08:30:02 PDT
