[AMBER] Turning initial velocity off for continuous MD runs

From: Aanshi Gandhi <aanshi.gandhi.mail.utoronto.ca>
Date: Tue, 9 Mar 2021 17:35:24 +0000


I am trying to run 50 ns MD simulation on a protein, and due to its large size I decided to split up the production steps into smaller increments with each subsequent run using the restart file from the former to continue. As a result, it would be meaningful for me to turn the ig flag “off” so that the initial velocities of each run is not determined at random but rather using the velocity from the former step. As per my understanding of reading the Amber manual, the two flags in addition to ig=0 that would affect this would be ntx=5 and irest=1. However even with these changes, it seems as though the initial velocities are chosen at random (based on how the RMSD plot looks). I have also seen in other answers of manually selecting a number for ig so that they all have the same velocity however, I wasn’t sure if that would solve my problem since the velocity still wouldn’t be a continuation of the previous run.

I’d really appreciate any insight into how to turn the random initial velocities off or if I’ve made any errors on my part. I have attached one of the MD input files (they are all the same) [“prod1.in”], the submission script [“runmd_script.sh”] and the RMSD plot [“rmsd3.agr”] for your convenience.

Thank you,
Aanshi Gandhi (she/her)

AMBER mailing list

Received on Tue Mar 09 2021 - 10:00:02 PST
Custom Search