AMBER Archive (2003)

Subject: Re: AMBER: MeCNBOX

From: James W. Caldwell (jimc_at_stanford.edu)
Date: Thu Sep 25 2003 - 16:04:03 CDT

I've made up several boxes of solvent and can tell you that (especially
with very non-polar solvents), it is almost an art to coax a crude guess
structure to an equilibrated box. You need to make changes in very
tiny steps (10-20 degrees) with long equilibration at each Temperature.
Turning down the time step to 0.5fsec can help too.

jim

On Thu, 2003-09-25 at 13:47, northrop_at_chem.ucla.edu wrote:
> The program fails in the constant pressure part. My value for taup has been 2.0, so I'll make
> that larger and see how things turn out. Here's a copy of my constant pressure input file that
> failed:
> &cntrl
> imin = 0, irest = 0, ntx = 1, iwrap = 1,
>
> ntpr = 100, ntave = 0, ntwr = 100,
>
> ntf = 2, ntc = 2,
>
> ntt = 1, tempi = 300.0, temp0 = 300.0,
>
> ntp = 1, pres0 = 1, taup = 2.0,
>
> ntb = 2,
>
> nstlim = 200000, dt = .001,
>
> nsnb = 100,
> &end
> Also, one other thing I've noticed is that when I solvate the 10 Å box of MeCN in leap, the MeCN
> units are in a very regular grid pattern and spaced relatively far appart. I imagine that once I
> start doing constant pressure dynamics they quickly try to cluster together and maybe the error
> message is due to the sudden change in the periodic boundary, but I'm not sure if that's the
> problem. I'll change taup to 5 (and higher if necessary). Thanks for the help!
> Brian Northrop
>
> "David A. Case" <case_at_scripps.edu> said:
>
> > On Thu, Sep 25, 2003, northrop_at_chem.ucla.edu wrote:
> >
> > > Amber users - I'd like to run some simulations in an acetonitrile solvent
> > > but I don't know how to make a pre-equilibrated solvent box similar to those
> > > that exist for CHCl3, water, etc. The parameters I'm using for acetonitrile
> > > are those from the six-site model of Jaime et. al. (JOC, 21, 10, 901- 908).
> > > My procedure for trying to equilibrate a box of acetonitriile is as follows:
> > > in leap, I set the restype of MeCN to solvent and then solvate a 10 Å box on
> > > MeCN 1000 step steepest descent minimization 20 ps constant volume run to
> > > raise the temp to 300 k 200 ps constant pressure run to equilibrate
> > > Unfortunately the program always fails with the error message "EWALD BOMB in
> > > subroutine, ewald_list, volume of ucell too big, too many subcells, list
> > > grid memory needs to be reallocated, restart sander." When I look at the
> > > restart file, there are large voids of no solvent within the periodic
> > > boundary. Any help anyone could give me about how to make a
> > > pre-equilibrated MeCNBOX would be greatly appreciated.
> > >
> >
> > Does the program fail in the constant pressure part? What value of taup are
> > you using? If it is less than 5 ps or so, you might try making that larger.
> > Otherwise, post the input files of something that fails, and Mike will get it
> > fixed right away :-)
> >
> > ..dac
> >
> > --
> >
> >
> ===========================================================
> =======
> > David A. Case | e-mail: case_at_scripps.edu
> > Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> > The Scripps Research Institute | phone: +1-858-784-9768
> > 10550 N. Torrey Pines Rd. | home page:
> > La Jolla CA 92037 USA | http://www.scripps.edu/case
> >
> ===========================================================
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>
>
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>
>
>
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-- 
James W. Caldwell					650-724-5322
Department of Chemistry
Stanford University

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