SMD in NAMD

From: Madhulika Gupta (gmadhulika1909_at_gmail.com)
Date: Sat Apr 23 2016 - 05:15:34 CDT

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Dear All,
How many SMD runs should be averaged over to obtain adsorption energies for
1. sulphur adsorption on metal surface
2. protein adsorption on a metal surface

On reading the literature, I find that some papers average over by doing
many runs by varying SMDVel or SMDk or SMDDir or the starting initial
positions. Then these SMD runs are repeated 3-4 times with different seed
values. However, some papers just use one single SMD simulation to
calculate the adsorption energy.
I am confused as to what is the correct method?
Can I average over 15 runs (with different starting positions) and repeat
each run 3 times with different seed values?

Any help would be highly appreciated.

Thanks in advance
Madhulika

-- 
Madhulika Gupta
Research Scholar
Department of Chemistry
Indian Institute of Technology, Delhi
New Delhi-110016

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