RE: Basic question about steered moledular dynamic(SMD) simulation

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon May 29 2006 - 09:51:02 CDT

I'm not sure what you mean by resultant force, but yes, it is the SMD spring
force.

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of ???
Sent: Monday, May 29, 2006 3:54 AM
To: JC Gumbart
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: Basic question about steered moledular dynamic(SMD)
simulation

Very thanks for your reply.
I have another small question.When do cv smd ,it output the "the center of
mass of the restrained atoms,and the current force applied to the center of
mass".Is the "current force " the "resultant force" or the "SMD spring"
force applied to the mass of center ???

? ??? 29 ?? 2006 13:36,JC Gumbart ??:
> The dummy atom moves v*t. The real atom moves according to the
> potential U = k*(r.n - vt)^2 (n is the unit vector direction).
>
> On May 29, 2006, at 12:49 AM, ??? wrote:
> > -----BEGIN PGP SIGNED MESSAGE-----
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> > HI,all
> > I have a basic question about SMD simulation.If I only tag one atom
> > named "atom1"to be applied SMD force.The SMDvel is "v" ,and the SMD
> > simulation time is "t",is this mean the "atom1" move distance is
> > "v*t" or the
> > SMD "dummy atom" move distance is "v*t"??
> > - --
> > office phone:84110036
> > Bioinfomatics SYSU
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-- 
office phone:84110036
Bioinfomatics SYSU

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