On 7/25/14, 8:10 AM, Tamas Karpati wrote:
Dear Justin,
Thank you for your quick answer.
Same with GROMACS-4.6.6: core-to-shell distance
must be >0 to not crash. My crystal is expected to be polarized
Does your topology specify the proper intramolecular exclusions? What is(are)
the molecule(s)?
(metallic and oxygen sites are the victims of this model).
The *.mpd file being used is:
# nstcalcenergy = 1 ; 4.6.6 claims this necessary, 4.6.3 didn't need it
Definitely true.
# integrator = steep
# vdw-type = cut-off
# coulombtype = pme
# nsteps = 10
# periodic-molecules = no
# cutoff-scheme = group
# ns-type = grid
# emtol = 10 ; default=10 kJ/mol/nm
# niter = 10000 ; default=20
# ;fcstep = ; default=0 ps^2 ; not quite clear what it is
# rlist = 1.0
# rcoulomb = 1.0
# rvdw = 1.0
# pbc = xyz
# nstxout = 1 ; wouldn't emit pos for each, though
# nstfout = 1 ; -"-
# nstlist = 1000 ; avoid it, no bonds at all
Try nstlist = 1. The shell positions are solved via SCF (EM), so you need to
update the neighbor list very frequently.
-Justin
# nstlog = 1
# ;pcoupl = no ; used to switch cell-optimization on/off
Best regards,
toma
On Fri, Jul 25, 2014 at 1:48 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 7/25/14, 7:43 AM, Tamas Karpati wrote:
Dear all,
I have two questions about geometry optimization of a crystal
with polarization via the core/shell model. I'm creating *.gro and
*.top files "by hand" and compile them with *.mdp to *.tpr via
GROMPP. My FF is also made by hand (simply because i need
to learn GROMACS). I have learnt on this list that with Buckingham
potentials I need to use the group rather than the Verlet scheme.
(1/2) Letting some of all atoms be polarizable through applying
shell particles made MDRUN segfault like this:
# ...
# Reading file AAA_opt.tpr, VERSION 4.6.3 (single precision)
# Using 2 MPI threads
#
# Steepest Descents:
# Tolerance (Fmax) = 1.00000e+01
# Number of steps = 10
# Segmentation fault1.0e-02 nm, Epot= -nan Fmax= 3.76506e+03,
atom= 1357
I imagined some divison by zero situation not handled and have put
some "random noise" on the shell particles' position so they do not
anymore start exactly at the atomic sites (meaning nonzero distances).
Seemed to work, at least no further crashes. Only energies and forces
seem very high:
# Steepest Descents:
# Tolerance (Fmax) = 1.00000e+01
# Number of steps = 10
# Step= 0, Dmax= 1.0e-02 nm, Epot= -1.36425e+07 Fmax= 2.99600e+05,
atom= 160
# Step= 1, Dmax= 1.0e-02 nm, Epot= -1.62080e+07 Fmax= 1.25769e+06,
atom= 160
# Step= 2, Dmax= 1.2e-02 nm, Epot= -1.95965e+07 Fmax= 6.87820e+08,
atom= 2759
# Step= 3, Dmax= 1.4e-02 nm, Epot= -2.02902e+07 Fmax= 1.30719e+09,
atom= 468
# Step= 8, Dmax= 1.1e-03 nm, Epot= -2.18970e+07 Fmax= 5.77722e+09,
atom= 1095
# Step= 10, Dmax= 6.5e-04 nm, Epot= -1.96952e+07 Fmax= 3.92889e+08,
atom= 1096
# Energy minimization reached the maximum numberof steps before the
forces
# reached the requestedprecision Fmax < 10.
My question is the following.
Is it (randomized shell positions) a correct procedure with GROMACS?
(2/2) Changing from a randomized x/y/z set to a fixed distance at
a random direction for the shell particles led to another unexpected
result.
I scanned a range between 1e-4 to 0.1 nm and noticed that
the final core-to-shell distance is a function of the starting one.
I used niter = 10000 (note: the default is 20) as i noticed in an MD
type of job that 20, 100 or 1000 steps were insufficient for the shells
to relax within default tolerance. The cell size was ca. 3x3x3 nm.
Please provide a full .mdp file; other settings are very relevant.
My question is the following.
What would be the appropriate core-to-shell distance to apply?
The equilibrium distance for core-shell bonds should be zero, deviations
from this non-polarized state account for the polarization energy.
I appreciate any help so thanks in advance.
Upgrade to 4.6.6; there have been issues with shells that have been fixed
since 4.6.3.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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