[gmx-users] Problem while equilibrating system with frozen groups
arnabmukherjee249 at gmail.com
Tue Sep 11 23:51:59 CEST 2018
Thank you very much for your suggestion. I will try using atom restraints
and check if the pressure coupling works properly.
Thanks and regards,
On Sep 11, 2018 10:33 AM, "Peter Kroon" <p.c.kroon at rug.nl> wrote:
> Hey Arnab,
> Why do you freeze atoms instead of putting position restraints? Why not
> let the loose entirely? Freezing creates large artefacts.
> Second, 4 ns equilibration is *way* too short.
> Lastly, see http://www.gromacs.org/Documentation/Terminology/Pressure
> On 10-09-18 19:01, ARNAB MUKHERJEE wrote:
> > Hi,
> > I am simulating DNA (infinite) protein Martini system with electric
> > I have 2 systems, for 1 complete DNA is frozen and for the 2nd one, only
> > 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
> > for the completely frozen DNA with 3 dimensions frozen? Since the DNA is
> > infinite I use semi-isotropic pressure coupling keeping the
> > along Z 0. So the pressure coupling options in my .mdp file looks like
> > :
> > 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.
> > plotted the pressure and the average pressure is 9.15 bar, while the
> > 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
> > 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),
> > 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
> > from the target pressure.
> > I am now running these equilibration runs for longer (4 ns), to see if
> > helps to get the average pressure closer to 1 bar. Normally when all
> > are free what I found was 0.5 ns was enough to get average pressure 1
> > and equilibrate the system. But I don't understand what is the problem I
> > 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,
> > Regards,
> > Arnab
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