[gmx-users] Problem while equilibrating system with frozen groups

ARNAB MUKHERJEE arnabmukherjee249 at gmail.com
Mon Sep 10 18:52:11 CEST 2018


I am simulating DNA (infinite) protein Martini system with electric field.
I have 2 systems, for 1 complete DNA is frozen and for the 2nd one, only 4
atoms of the DNA is frozen. When I perform NPT equilibration for the
complete DNA frozen system, it shows me this error :

 Fatal error:
4442 particles communicated to PME rank 24 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension y.
This usually means that your system is not well equilibrated.

But it runs fine for the other system with 4 DNA atoms frozen. For the
completely frozen DNA, if I freeze only 2 dimensions, letting 1 dimension
free it runs without complaining. I do not understand why it shows problem
for the completely frozen DNA with 3 dimensions frozen? Since the DNA is
infinite I use semi-isotropic pressure coupling keeping the compressibility
along Z 0. So the pressure coupling options in my .mdp file looks like this

freezegrps = DNA
freezedim = Y N Y

; Pressure coupling is off
;pcoupl     = no        ; no pressure coupling in NVT
Pcoupl     = parrinello-rahman
Pcoupltype  = semiisotropic
tau_p       = 5.0
compressibility = 3e-4 0
ref_p       = 1.0 1.0
refcoord_scaling = all

I tried it for finite DNA too and it shows same problem for completely
frozen DNA.

I ran the completely Frozen DNA system keeping 1 dimension free, and
freezing the other 2 dimensions. I ran the equilibration run for 500 ps. I
plotted the pressure and the average pressure is 9.15 bar, while the target
pressure that I had put in the .mdp file is 1 bar. So there is a large
difference. I was searching regarding this problem, and I found that I need
to use "energygrp-excl" for frozen groups. So I ran the completely frozen
DNA system with  energygrp-excl = DNA, using cutoff-scheme = group (since
energygrp-excl is not supported in Verlet in my gromacs version 5.0.6), and
the average pressure I get is again 9.28 bar. For the system with 4 DNA
atoms frozen, the average pressure shows 5.17 bar, which is still different
from the target pressure.

I am now running these equilibration runs for longer (4 ns), to see if that
helps to get the average pressure closer to 1 bar. Normally when all atoms
are free what I found was 0.5 ns was enough to get average pressure 1 bar,
and equilibrate the system. But I don't understand what is the problem I am
facing here with frozen atoms?

I turn off the electric field during the equilibration runs.

I would highly appreciate any help!

Thank you very much,



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