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

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon May 29 2006 - 12:01:21 CDT

Ah, I see.

The force output to the log file is JUST the smd spring force.

-----Original Message-----
From: ??? [mailto:lsp04whm_at_zsu.edu.cn]
Sent: Tuesday, May 30, 2006 11:23 AM
To: JC Gumbart
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: Basic question about steered moledular dynamic(SMD)
simulation

I mean the "SMD spring" apply a force on the SMD tagged atom "atom1",and the

atom linked to "atom1" will also apply force on it(example,on peptide
backbone ). So the "output force" is the "SMD spring" force ,or the force
applied on "atom1" together ???Maybe i didn't describe clearly,the resultant

force means "the resultant of forces" or "join forces".

在 星期一 29 五月 2006 22:51,您写道:
> 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-----
> > > Hash: SHA1
> > >
> > > 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
> > > -----BEGIN PGP SIGNATURE-----
> > > Version: GnuPG v1.4.3 (GNU/Linux)
> > >
> > > iD8DBQFEeot9JUbxwlqZ84QRAsI7AJ9kHILJsLJwhWOx68DiIR4kPnRd2wCfX/L+
> > > V8re4PTWim0Fc/R7NNcTEes=
> > > =B7qc
> > > -----END PGP SIGNATURE-----

-- 
office phone:84110036
Bioinfomatics SYSU

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