I believe you’re looking for ramdmaxdist which is set in angstroms of how far the CoM between the ligand and the chosen protein center of mass distance is that turns off the simulation (which is generally what you want since you’re using RAMD to try to estimate an off rate).
For the most basic run you’’ll need to set the following variables: ramdboost, ramdint, ramdligmask, ramdprotmask, ramdmaxdist.
If you never reach the ramdmaxdist, the run will finish when nstlim is hit.
-Charlie
From: 田佳琪 <tianjq.sjtu.edu.cn>
Reply-To: AMBER Mailing List <amber.ambermd.org>
Date: Monday, December 6, 2021 at 2:02 AM
To: "amber.ambermd.org" <amber.ambermd.org>
Subject: [AMBER] about RAMD
Dear Amber Users and Developers,
I run RAMD with amber20,but I don't know which parameter represent the threshold distance (rmin).
In RAMD, if the ligand does not reach the threshold distance (rmin), a new, randomly chosen direction is given to the force on its center of mass; otherwise, the force direction is maintained.
Please help, thanks!
with regards
Tian
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Received on Mon Dec 06 2021 - 09:00:02 PST
