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
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Received on Mon Aug 06 2018 - 19:00:03 PDT
