Re: AMBER: Heat of Vaporization

From: Thomas Cheatham III <>
Date: Tue, 15 May 2007 10:37:01 -0600 (Mountain Daylight Time)

> > I would like to know how to do a md simulation with cutoff set to 0.
> What happens if you just try it? Comment out the section in mdread.f
> that stops because this is "unreasonably small".

Although DAC's advice to try it is sound, this may be a little more
complicated as the 1-4 nonbonded interactions are not subject to a cutoff
according to my quick read of the code; in any event, I doubt that you
could run Ewald/PME with a zero cutoff.

What I would do is run a short cutoff and then use the NMROPT=1 options
and the weights to effectively turn-off the nonbonds... Alternatively, I
would simply zero the charge and vdw parameters when building my prmtop
and run with a short cutoff.

 &wt type = 'NB', value1=0.0,
 &wt type = 'END',

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Received on Wed May 16 2007 - 06:07:33 PDT
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