[AMBER] COM pulling in direction

From: Meng Wu <wumeng.shanghaitech.edu.cn>
Date: Tue, 7 Aug 2018 01:51:28 +0000

Deal all,

    Just a quick question, could Amber16 support COM pulling in direction? I have read the web tutorial (https://github.com/callumjd/AMBER-Umbrella_COM_restraint_tutorial) , it's pulling based on distance. In my case, the small molecule that I want to pull is initially in the middle of the channel protein, so I divided the whole SMD into two parts, the up-direction part and down-direction part along z axis, then if I did the umbrella sampling based on distance, WHAM would give the wrong results. So I am wandering if it's possible to do COM pulling in direction, could anybody give me some suggestions? Thanks in advance!

All the best,
Meng Wu


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 06 2018 - 19:00:03 PDT
Custom Search