[gmx-users] Simulation getting slower and ultimately crashing

soumadwip ghosh soumadwipghosh at gmail.com
Wed Apr 27 11:22:52 CEST 2016

     I am simulating a nucleic acid in the presence of a 15X15 single
walled carbon nanotube using CHARMM 27 force field and TIP3P water model.
In my previous published work, I did the simulation inside a cubic box and
everything ran fine but as of now whenever I am switching over to a
triclinic box the simulation goes smoothly up to NPT (7 ns) step but it
crashes down during production run printing the following error:

"inconsistent dd boundary staggering limits gromacs"

It is telling about the improper equilibration of the system and its
blowing up. What might be the reason for such instability of the system?
Also the simulation gets slower and slower before crashing down. I am using
GROMACS 4.5.6 on CenTOS.

I am uploading my files below for reference. One different thing (apart
from changing the box type) I have done is I have rotated the hybrid system
(nucleic acid+CNT) in y-axis using editconf and then defined the box type.
Apart from that every steps performed (and the parameter files) are
identical. I created the SWCNT topology using g_x2top with CHARMM 27
parameters. Any kind help will be appreciated.

cnt.itp file: https://drive.google.com/open?id=0B7SBnQ5YXQSLZ0k3QnJPaXBmbnc

the hybrid.pdb file (containing the NA+CNT):

the md.mdp file:

Thanks in advance

Soumadwip Ghosh
Senior Research Scholar

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