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

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue May 30 2006 - 11:47:58 CDT

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, 吴洪明 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"????
>>
>> 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-----
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>>>>>>
>>>>>> iD8DBQFEeot9JUbxwlqZ84QRAsI7AJ9kHILJsLJwhWOx68DiIR4kPnRd2wCfX/L+
>>>>>> V8re4PTWim0Fc/R7NNcTEes=
>>>>>> =B7qc
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>
> --
> office phone:84110036
> Bioinfomatics SYSU

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