RE: question about SMD

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Aug 20 2019 - 14:55:31 CDT

Hi Maria,

10e-6=1e-5 Angstroms/step, 10e6=1e7 steps, so naively I'd expect 100Angstroms worth of motion. I see that your SMDVel is 1e-6, and over 10 million steps (10000000), that would get you a motion of 10 Angstroms. How many steps does the NAMD logfile say you took? I'm wagering its 10000000, not 1000000 like you are assuming.

-Josh

On 2019-08-20 13:49:13-06:00 owner-namd-l_at_ks.uiuc.edu wrote:

I run steered MD with the velocity 10E-6 ( SMDVel 0.000001 ) and k=0.2 (SMDk 0.2).

I find that my protein moves at a distance of 10A in 10E6 steps.

How could this happen? - I thought that the maximal distance it could move would be vt, which is 1 A per 10E6 steps in my case .

The dependence of the coordinate on the time-step is almost linear during the initial 10E6 steps.
Am I missing something?

Thanks,
Maria

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