AMBER Archive (2008)

Subject: AMBER: SMD-related questions

From: Alessandro Nascimento (al.s.nascimento_at_gmail.com)
Date: Mon Dec 29 2008 - 07:07:05 CST

Hi guys,

I have been through the manual but could not find the units of force
for SMD. I assume it is pN as in NAMD. Is that correct?

A second question is: the steering velocity is not set, as in NAMD, in
the simulation input file. I presume it is given by the steering
distance over the simulation time (r2a/nstlim). Is that correct?

Could someone also provide some references (or share personal
experiences) regarding the spring constant on SMD simulations
(especially in Amber FF)?

Thanks a lot in advance and a happy new year for all,

--alessandro
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