[AMBER] equilibration of Packmol generated boxes

From: Arkajyoti Sengupta <arkaseng.iu.edu>
Date: Wed, 28 Nov 2018 18:30:31 -0500

Hi Amber developers,

I'm trying to simulate metal ion complexation with organic molecules. I
have used Packmol to build a box containing the requisite number of ions,
counterions, organic molecule and water to make a solution with known
molarity. It has been pointed out in the ambermail list (
http://archive.ambermd.org/201104/0347.html) that the boxes created with
Packmol are not relaxed to the force field, so equilibration of the box is
suggested as in the amber tutorial.

I did the minimization and the equilibration as in amber tutorial. However,
on choosing a larger box, the equilibration results in vacuum bubbles
inside the box and the density drops throughout the NPT equilibration.

I tried another way by shrinking the box (to make it comparable to 55.55 M
for 1g/L density of water). The minimizations with pmemd gave the
following error:

cudaMemcpy GpuBuffer::Download failed an illegal memory access was

We tried sander and the minimizations got completed with sander. This was
followed by heating 0 to 300 K and equilibration of box in sander. The
simulations results in an equilibrated box with every species inside it.

Next, we wanted to use the generated equilibration rst for Production using
PMEMD. However, it still shouts:

cudaMemcpy GpuBuffer:: Download failed an illegal memory access was

For the production runs, we'll be running simulations in the order of
hundreds of ns which are done quickly using PMEMD code.

Please let us know of any alternatives or tweaking that can be done to use
the PMEMD code for the long runs for these simulations starting from
Packmol generated boxes or sander equilibrated geometries. Following are
the inputs:

a series of minimization with inputs:



imin=1, ntpr=400, ntwx=400, maxcyc=20000,

ncyc=12000, lj1264=1,ntmin=1

ntb=2,ntc=1, ntf=1, cut=12,


Heating at constant Pressure

heat NPT 200ps


  imin=0, ntx=1,

  nstlim=200000, dt=0.001,

  ntc=2, ntf=2, cut=12.0,

  ntt=3, gamma_ln=1.0,iwrap=1

  ntb=1, taup=5.0, tautp=0.5

  tempi=0.0, temp0=300.0,

  ntpr=4000, ntwx=4000, ntwr=4000,

 ioutfm=1, ntxo=2, ig=-1,






&wt type='END' /


equilibration for box


imin=0, ntpr=6000, ntwx=6000,ntwv=-1

ntx=1, irest=0,

tempi=300., temp0=300., ntt=3,

gamma_ln=5., ntb=2, ntp=1, taup=1.0, ioutfm=1, nstlim=150000

ntwr=1000, dt=.001, ig=-1,ntxo=2, dt=0.001, iwrap=1


ntc=2, ntf=2, cut=12.0, igb=0,pres0 = 1.0



Arkajyoti Sengupta, Ph. D.
Postdoctoral Researcher
Merz Group,
Department of Chemistry,
Michigan State University
578 S Shaw Ln, East Lansing,
MI 48824
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Received on Wed Nov 28 2018 - 16:00:02 PST
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