From: Jiten <>
Date: Sat, 11 Oct 2003 12:29:04 +0900


I have also faced this type of problems when I tried to equlibrate
acetonitrile in amber7. So I perform the equlibration at constant pressure
in amber6 without EWALD option. It works well though I got slightly lesser
density then the experimental value.

Best wishes,


----- Original Message -----
From: <>
To: <>
Sent: Saturday, October 11, 2003 9:31 AM
Subject: AMBER: MeCNBOX & EWALD bomb

> 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:
> &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 = 5.0,
> ntb = 2,
> nstlim = 400000, dt = .001,
> nsnb = 100,
> &end
> 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.
> thanks,
> Brian Northrop
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Received on Sat Oct 11 2003 - 04:53:01 PDT
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