# 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 - 03:48:41 CDT

Sorry ,not calculate from "F=k*d,d=[vt-(Rt-R0)n]^2".
But can "smd spring force" be calculated from "F=k*d,d=vt-(Rt-R0)n"????
>
> 在 星期二 30 五月 2006 01:01，您写道：
>
> > 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
```

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:43:39 CST