AMBER Archive (2003)

Subject: Re: AMBER: MeCNBOX

From: northrop_at_chem.ucla.edu
Date: Thu Sep 25 2003 - 15:47:03 CDT

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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