Re: [AMBER] constant pressure

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Sun, 4 Dec 2011 12:36:55 -0800

> I attached the output files in my earlier reply.

I rarely open attachments. Mdin files are small and worth comparing
in proximity to each other.

> My molecule is somewaht
> similar to plastocyanin as discussed in AMBER tutorial 4 instead of copper
> I have a K+ ion (non -bonded interaction with monomer) , I have non bonded
> parameters in my frcmod file while I construct the solvated box .

By the way, the standard ion vdw parameters are derived for interactions
with the water model, not the Amber residues and others parameterized
the same way. I've never seen anyone else stress this fact, but
here is a paper where it is investigated at length:

    Ion-Induced Stabilization of the G-DNA Quadruplex: Free Energy
    Perturbation Studies. W.S. Ross and C.C. Hardin
    Journal of the American Chemical Society 116, 6070 (1994).

> Is my error related to this intitial structure , I require to have a non
> bonded ion, how can I work with this in the input files while running MD.

A non-bonded ion is fine, see many studies of this. The first step of
triage is to rule out equilibration errors. Please re-read the below:

> > equilibration at 50K at constant
> > volume and then I turn on constant pressure equilibration
> Did you jump the temperature or change the time step between
> the two? I suggest pasting in all your mdin files to the response.
> Bill
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Received on Sun Dec 04 2011 - 13:00:02 PST
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