On 4/10/20 8:13 AM, Alex wrote:
Dear Justin,
Any comment please?
Sorry, haven't had power/network for a while due to some bad storms here.
GROMOS force fields are parametrized assuming all bonds are fixed, so
your constraints should be "all-bonds" not "h-bonds."
I would also suggest you thoroughly validate the quality of the epoxy
molecule topology against QM data and bulk-phase properties, if possible.
-Justin
Regards,
Alex
On Tue, Apr 7, 2020 at 5:38 PM Alex <alexanderwie...@gmail.com> wrote:
Thanks Justin for the response.
Please find below the mdp file.
The system is a thin film made out of a epoxy molecule, picture in be
below link, with water on top and bottom of the film. I even sometimes have
the same issue when I simulate the bulk of this system, I mean a cubic box
filled by this molecule and no water.
I got the force fields from the latest version of ATB repository by which
I have previously done some other simulation for the same molecule.
https://drive.google.com/open?id=1tJLxh9jQ2v5DDTrVR8IuQz40B3NN0zlb
%--------mdp-------
title = Thin-Film
integrator = md
dt = 0.002 ; 2 fs ;0.001 1 fs
nsteps = 25000000 ; 50 ns ;50000000 ; 50 ns
xtc-precision = 500 ; 1000
;nstlist = 40
%-----------------
;;in .trr file
nstxout = 3000 ; 6000
nstvout = 0
nstfout = 0
;;in energy file.log
nstlog = 2000 ; 4000
nstcalcenergy = 2000 ;4000
nstenergy = 2000 ;4000
;;in xtc file
nstxout-compressed = 0
;compressed-x-grps = non-Water
%-----------------
continuation = yes
gen-vel = no
constraint-algorithm = lincs
constraints = h-bonds
cutoff-scheme = Verlet
coulombtype = PME
rcoulomb = 1.4
vdwtype = Cut-off
rvdw = 1.4
DispCorr = EnerPres
tcoupl = v-rescale
tc-grps = system
tau-t = 1.5
nhchainlength = 10
ref-t = 298.15
pbc = xyz
pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
tau_p = 2.5
compressibility = 4.5e-5
ref_p = 1.0
refcoord-scaling = com
energygrps = thin_film SOL
comm-mode = Linear
nstcomm = 100
comm-grps = Thin_fiml SOL
%-------------------------
Thank you
Alex
On Tue, Apr 7, 2020 at 5:06 PM Justin Lemkul <jalem...@vt.edu> wrote:
On 4/7/20 5:00 PM, Alex wrote:
Dear all,
After minimization and equalizations using nvt (v-rescale) and npt (both
berendsen and ;Parrinello-Rahman), a simulation of mine could run well
for
200 ns using dt =0.001 while it would crash after 3 ns If I used dt =
0.002
with the particles communication fatal error.
Fatal error:
2 particles communicated to PME rank 12 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.
So, if the system would not be well equlibrated, then I would expect
that
with dt = 0.001 the simulation wouldn't run well for 200 ns. But I
expect
that it also crashes for example around 6 ns as the with the dt = 0.002
the
simulation last only 3 ns.
Any comment that helps to understand the problem would be highly
appreciated.
Please provide a description of what your system is and a full .mdp
file. While most of the time these crashes come from poor equilibration,
an inadequately parametrized topology or bad combination/misuse of
algorithms can also cause crashes.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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