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

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed May 31 2006 - 09:19:11 CDT

You have to remember, force is a vector. In this simple case where you are
pulling along one axis only, this is basically correct. Otherwise, you will
have to consider more carefully how you get the force.

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of ???
Sent: Wednesday, May 31, 2006 1:45 AM
To: JC Gumbart
Cc: namd-l_at_ks.uiuc.edu
Subject: Re: namd-l: Basic question about steered moledular dynamic(SMD)
simulation

Sorry , I didn't catch you mean very much .
F=-grad U,and "spring force" can also calculated from multiply
the "spring constant(k)" and the "spring extention(d)".this result F=k*d.

If I constrain the "atom1"on x axis ,apply SMD force on "atome1" by
setting SMDdir "1 0 0" ,so the "atom1" move along x axis.if "SMDVel"
were "v",smulation time were "t",the initial "atom1" coordinate were for
example {5 0 0},through time "t",its coordinate were for example {10 0 0},so

the "spring extention(d)" can calculate from equation :d=[vt-(10-5)].Here
came my question:can "SMD spring force" calculate from F=k*[vt-(10-5)]??
Thanks
? ??? 31 ?? 2006 00:47,???:
> Almost.
>
> F = -grad U. So it is that factor you gave multiplied by the
> gradient of [(R-R0).n] which I believe just gives you the unit vector
> n again.
>
> On May 31, 2006, at 3:48 AM, ??? wrote:
> > 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"????
> >
> >> ? ??? 30 ?? 2006 01:01,???:
> >>
> >>> 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".
> >>>
> >>> ? ??? 29 ?? 2006 22:51,???:
> >>>
> >>>> 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

```--
office phone:84110036
Bioinfomatics SYSU
```

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