Re: minimization of the squared gradient

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon May 19 2008 - 09:20:17 CDT

Ah, sorry, misread the question. No, I'm not aware of a way to do this
in namd; you'd need to write a different minimization routine;.
Peter

Krishnan, Marimuthu wrote:
> Hi Peter,
>
> Yes. The "minimize" command minimizes the potential energy (U) of the system. I would like to minimize the squared gradient ([dU]^2) of the potential energy. This way, the system can be quenched to a stationary point (This can correspond to a minimum or a saddle).
>
> Thanks.
> Krishnan
>
> *************************************************
>
> Dr. Marimuthu Krishnan
> Postdoctoral Research Scholar,
> Center for Molecular Biophysics,
> Oak Ridge National Laboratory,
> PO Box 2008 MS6164,
> Oak Ridge, TN 37831-6164,
> Tel : 001-865-574-6123
> Fax : 001-865-576-7651
> E-mail : krishnanm_at_ornl.gov
>
> *************************************************
>
> ________________________________
>
> From: owner-namd-l_at_ks.uiuc.edu on behalf of Peter Freddolino
> Sent: Mon 5/19/2008 7:40 AM
> To: Krishnan, Marimuthu
> Cc: namd-l_at_ks.uiuc.edu
> Subject: Re: namd-l: minimization of the squared gradient
>
>
>
> Hi Krishnan,
> it isn't exactly clear to me from what you wrote: Do you want something
> different from what you get by using the "minimize" command?
> Best,
> Peter
>
> Krishnan, Marimuthu wrote:
>
>> Dear all,
>>
>> Is it possible to use NAMD to minimize the squared gradient of the potential energy? I would appreciate If someone could provide me a script for doing this.
>>
>> Thanks.
>> Krishnan
>>
>> *************************************************
>>
>> Dr. Marimuthu Krishnan
>> Postdoctoral Research Scholar,
>> Center for Molecular Biophysics,
>> Oak Ridge National Laboratory,
>> PO Box 2008 MS6164,
>> Oak Ridge, TN 37831-6164,
>> Tel : 001-865-574-6123
>> Fax : 001-865-576-7651
>> E-mail : krishnanm_at_ornl.gov
>>
>> *************************************************
>>
>>
>
>
>
>

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