[gmx-users] Energy Minimization/ NpT settling problem

pcl pcl at uab.edu
Fri Dec 21 00:27:26 CET 2012

A couple of things:

1. Are your cutoffs appropriate for OPLS_AA? Even if you fix any code problems and using the wrong cutoffs, your results will not be meaningful...
2. How are you generating your box/filling it with molecules? There are indications that your original box is too small, or that there are clashing atoms in the original configuration, since with a much bigger box you don't seem to have problems except for particles moving too rapidly for domain decomposition to handle (perhaps there is a cutoff/coupling problem).
2b: what is atom 13090 and what is in its vicinity?
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of emmanuelle [E.A.Y.Masy at student.tudelft.nl]
Sent: Thursday, December 20, 2012 2:31 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] Energy Minimization/ NpT settling problem

I am trying to simulate a system consisting of 1790 molecules of
monoethanolamine (MEA), 203 molecules of CO2 and 18210 molecules of
water. After having generated my box and set the density to 1000g/l
using editconf, I am facing a problem with the energy minimization
step. It does not converge to the tolerence I give (Fmax<500kJ/mol). I
get this message:

Steepest Descents converged to machine precision in 199 steps,
but did not reach the requested Fmax < 500.
Potential Energy  = -9.27407663461033e+05
Maximum force     =  2.07667591793109e+06 on atom 13090
Norm of force     =  1.06912622245517e+04

Since no problem occurs when I simulate CO2 with water only, I think
the problem comes from MEA for which I apply an OPLS_AA force field. I
tried lots of different initial configurations for MEA, using
structures developed with the Avogadro program and structures from
data bank found on the net. All of them result in the same convergence
problem. I don't think there is an issue in my mdp file as I use it
for other simulations which work well. It is as follow:

title           = Minimization  ; Title of run
define          =-DFLEXIBLE

; Parameters describing what to do, when to stop and what to save
integrator      = steep         ; Algorithm (steep = steepest descent
emtol           = 500.0         ; Stop minimization when the maximum
force < 500.0 kJ/mol
emstep          = 0.001          ; Energy step size
nsteps          = 100000        ; Maximum number of (minimization)
steps to perform

; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
nstlist         = 1             ; Frequency to update the neighbor
list and long range forces
ns_type         = grid          ; Method to determine neighbor list
(simple, grid)
rlist           = 1.0           ; Cut-off for making neighbor list
(short range forces)
coulombtype     = PME           ; Treatment of long range
electrostatic interactions
rcoulomb        = 1.0           ; long range electrostatic cut-off
rvdw            = 1.0           ; long range Van der Waals cut-off
pbc             = xyz           ; Periodic Boundary Conditions (yes/no)

I also tried another approach: I inserted the molecules in a much more
bigger box and performed the energy minimization of this system with a
very low density. This could converge. Afterwards, I run an npT
simulation with a high pressure (10 bar) such that the box shrinks and
that the system reachs the good density. At that step, the following
error came out:

 Making 1D domain decomposition 12 x 1 x 1
starting mdrun 'CO2 in MEA at 303K'
5000 steps,      5.0 ps.
^Mstep 0imb F  4% ^Mstep 100, remaining runtime:   132 s
step 134: Water molecule starting at atom 24060 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates

Program mdrun_d, VERSION 4.5.5
Source code file: pme.c, line: 538

Fatal error:
1 particles communicated to PME node 7 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension x.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

Can someone tell me where I am making any mistake and why is my system
not converging?

Thanks in advance,

MSc student -TU Delft

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