AMBER Archive (2007)

Subject: Re: AMBER: Heat of Vaporization

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Tue May 15 2007 - 11:37:01 CDT

> > 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,
 &end
 &wt type = 'END',
 &end

--tec3
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