Re: Creating bonds during a run

From: Praveen Agrawal (praveen_at_scfbio-iitd.res.in)
Date: Wed Jan 21 2009 - 04:18:43 CST

Hi Jerome,
My take is that it will also depend on the Hs which are being 'eliminated'
for the bond formation. Else the two (assuming single bond) Hs will never
let the two atoms come near by!

Praveen

> Hi Marcin,
> If you are dealing with few particles, you could also script this in Tcl.
> Jerome
>
> On Mon, Jan 12, 2009 at 11:09 AM, Axel Kohlmeyer <akohlmey_at_cmm.upenn.edu>
> wrote:
>> On Mon, 12 Jan 2009, Marcin S. wrote:
>>
>> MS> Hello,
>> MS>
>>
>> MS> Is there any way to create bonds during a NAMD run? Or, is it
>> MS> possible to "glue" two particles together during a run?
>>
>> how about adding a restraint and cranking up the force
>> constant during the run?
>>
>> cheers,
>> axel.
>>
>> MS>
>> MS> Thanks,
>> MS> Marcin S.
>>
>>
>>
>>
>> --
>> =======================================================================
>> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
>> Center for Molecular Modeling -- University of Pennsylvania
>> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
>> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
>> =======================================================================
>> If you make something idiot-proof, the universe creates a better idiot.
>

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