AMBER Archive (2002)

Subject: Re: using SHAKE for solvent only

From: David A. Case (case_at_scripps.edu)
Date: Mon Nov 25 2002 - 12:17:54 CST

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 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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