On 4/4/17 9:45 AM, Dayhoff, Guy wrote:
On 4/4/17 9:31 AM, Dayhoff, Guy wrote:
On 4/3/17 2:33 PM, Dayhoff, Guy wrote:
Hi,
I?m receiving a couple (~15) EM did not converge warnings as well as a few (~3)
1,4 interaction
warnings during my run. It looks like it starts down the path to blowing up but
recovers. Is this ?recovery?
system dependent? Should I take these messages (even without the subsequent
crash) to indicate an
underlying issue with my system/topology or equilibration? I?m not ignoring or
circumventing any warning
during pdb2gmx, or any other commands.
For more context: I?m running the Drude-2013 forcefield, with a dt of .5fs
emtol of 1.0 and niter of 150
using the V-rescale thermostat and Berendsen pressure coupling while my systems
cell shape relaxes
as a continuation from position restrained NVT then NPT ensembles. The starting
structures were minimized
in vacuum, then solvated and minimized once again prior to the posres
equilibration.
Such a short dt and strict niter should not be necessary in practice. The
failure of SCF to converge/LINCS warnings is what we typically refer to as
polarization catastrophe, so your system is on the brink of instability. This
is one of the inherent problems of SCF in polarizable systems; it often fails to
converge and leaves the system potentially unstable. The reflective hardwall is
much more reliable (and faster). If the instability is happening in your
equilibration, that may be OK but it is something you should try to troubleshoot
to make sure there's nothing else going wrong.
-Justin
--
Got it. I have been spending some time investigating the issue i?m having and
after reading shellfc.cpp I was pretty confident the issue was with SCF not
converging,
and so my niter and dt were an attempt at looking into that.
The workflow i?ve been trying to use is?
EM -> Solvate -> EM -> posres NVT V-rescale -> posres berendsen NPT isotropic 1bar
w/ V-rescale tcoupl ->
berendsen NPT semi-isotropic various pressures w/ V-rescale tcoupl
then once my cell shape has reached an equilibrium I finally switch to NH
thermostat and PR barostat for
the production run.
If I switch to employing the hardwall (and the lagrangian dynamics for drudes)
then I understand it is not
compatible yet with NPT ensembles. So, if I change my work flow as follows
would it be appropriate still?
EM->Solvate->EM->posre NPT isotropic 1 bar w/ V-rescale tcoupl->NPT
semi-isotropic varying pressures
w V-rescale tcoupl until cell shape is equilibrated using PR barostat, then
switch to NVT without pcoupl
to use the hardwall during my production run?
For some reason, i?ve got this idea that I need to be tcoupling and pcoupling
during my production runs
so i?ve been apprehensive to do this.
If you want an NPT ensemble during dynamics you're going to have to use NAMD,
CHARMM, or OpenMM. I haven't coded the barostat yet (fixing the DD bugs has
been more important). You can equilibrate with SCF under NPT and get a suitable
density, then switch to NVT, but your use of semi-isotropic coupling suggests a
membrane system? In that case, I would not use NVT during production as you
will be simulating a constant area, which may not be appropriate.
I?ve parameterized beta-cellulose and then an additional modified form of
beta-cellulose for the FF
and i?m looking at the packing behavior of a bundle of strands under the
different pressures in water.
Everything seems to be proper apart from encountering the polarization
catastrophe randomly,
often times I can restart a downed run and it will move beyond the previous
crash point, but this
is tedious and even when I wrote a script to do it for me I found that
eventually there was a point
of no return, even if I used the prev_cpt.
If you have this many crashes, your physical model is not suitable. You need to
revisit the parametrization before even thinking about more simulations. An
occasional convergence failure with SCF during equilibration is not worrisome,
continual problems indicate a bad model. Your tiny time step and large niter
value were clues that this is the case.
-Justin
Okay thanks. To be clear I did use a dt of 1fs and 1.25fs with niter = 50 in my
initial runs which all
went through EM, posres NVT and NPT with scf just fine and then began to have
issues after removing
the posres. Now that i’m writing this I suppose that is also an indication that
the issue lies in my parameters
and the behavior of the strand once it’s allowed to move freely?
Yes, precisely. If your run only continues if it's restrained or forced through
by repeated restarts, it's a bad simulation.
For what it's worth, carbohydrate linkages are very complex and we're still
working on getting all aspects of this right. It's no surprise you're facing
issues. We've been working on disaccharides of all types for months :)
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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