Re: using SHAKE for solvent only

From: David A. Case <>
Date: Mon 25 Nov 2002 10:17:54 -0800

On Mon, Nov 25, 2002, hagop demirdjian wrote:
> I am currently studying HF in a box of TIP3P water and want to get the
> IR spectrum of HF. In order to do so I need to let the HF bond free of
> constraints. But TIP3P model was designed to have fixed bondlenght so I
> was wondering if it would change the results a lot if I leave it flexible.
> I would like to run both simulations (H2O with varying/fixed bondlenght)
> in order to do so, I would like to know if there is a way to apply SHAKE
> to the solvent only ?

Only by trickery: define the "H" in HF to be a new atom type, with a mass
of 1.008 but whose name does not begin with "H". I think then you would
not get SHAKE for that atom, but would get it for the waters (where you want
it). Be sure to check carefully in a short run (or examine the prmtop file)
to make sure it is doing what you want.

..good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Mon Nov 25 2002 - 10:17:54 PST
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