From owner-chemistry -8 at 8- ccl.net Tue Jan 17 03:05:00 2006
From: "Mgr. Lubos Vrbka lubos.vrbka:_:uochb.cas.cz" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL: Heating Locally in MD
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X-Original-From: "Mgr. Lubos Vrbka" <lubos.vrbka#%#uochb.cas.cz>
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Date: Tue, 17 Jan 2006 07:44:02 +0100
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Sent to CCL by: "Mgr. Lubos Vrbka" [lubos.vrbka- -uochb.cas.cz]
hi,

> I am novice user here and would like to do some molecular dynamics calculation of an enzyme, with special requirement that only heating a part of the protein and freeze the rest. i.e., after minimizing and equilibrating the whole protein at 10K, only thermalize the active site of the enzyme to 300K.  
> 
> I am wondering which MD package could that. If possible, I prefer to free software such as TINKER. 
i think gromacs should be able to do that... and it is for free (GPL, 
iirc) as well.

regards,
lubos

-- 
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Mgr. Lubos Vrbka

Center for Biomolecules and Complex Molecular Systems
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic
Prague, Czech Republic

http://www.molecular.cz/~vrbka
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