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

From: q=E2=BA=E9=C3=F7?= (lsp04whm_at_zsu.edu.cn)
Date: Wed May 31 2006 - 00:05:38 CDT

I see.But can the "smd spring force" calculate
from "F=k*d,d=[vt-(Rt-R0)n]^2".

> 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
> >
> > 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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