From: <>
Date: Sat, 11 Oct 2003 00:31:46 -0000

Amber users,

I have posted about this problem before and I really appreciate all the help I've gotten, but I still
can't get a constant pressure dymanics simulation to run in an acetonitrile solvent. I obtained a
pre-equilibrated MeCN box (prep, box, frcmod) from Ricahrd Bryce's AMBER website (thanks for
the suggestion Pascal). I tested the solvent box by doing a simple minimization followed by
const. volume to warm to 300K and then a const. pressure simulation of just the MeCNBOX, but
it failed with the same "EWALD BOMD in subroutine ewald-list volume of ucell too big, too many
subcells list grip memory needs to be reallocated, restart sander" error. Looking at the restart
file I noticed that some of the solvent packs closer together while a few solvent molecules drift
away from the center, which causes the "volume of ucell too big" error. In order to try and
equilibrate a good MeCN box, I've been deleting solvent molecules that drift off, setting a new
box around those that have packed close to center (using "setbox UNIT centers"), rerunning
dynamics, and repeating. After doing this five times the constant pressure dynamics still fails
after 100-250 ps with the same error. Any time I try to run a simulation with a small molecule
solvated with the MeCN box, I get the same EWALD error and can see from the restart file that
some solvent molecules have packed close to the solute and a few others have started drifting
away (even when I solvate to only 2 away from the solute, trying to keep all the solvent near
the solute). Here is an example input file for one of the constant pressure simulations with a
small molecule in the MeCN box:
  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 = 5.0,

  ntb = 2,

  nstlim = 400000, dt = .001,

  nsnb = 100,
I'm hoping at this point that it's not a problem with the solvent box but with something in my
input file. Is there any way to do a constant pressure dynamics run and somehow still
constrain solvent molecules to stay within some boundary. Any help anyone could provide
would be greatly appreciated.

Brian Northrop

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Received on Sat Oct 11 2003 - 01:53:01 PDT
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