[gmx-users] periodic surface minimization
escajarro
juan-manuel.castillo at mv.uni-kl.de
Tue Sep 24 15:08:50 CEST 2013
Dear list members,
I am trying to simulate an infinite layer of quartz in Gromacs. Due to my
needs (afterwards I need to place a large molecule on top of it) the surface
must be at least 12x12 nm^2. I generated the input files from a pdb file of
the structure, and adapted the OPLS force field to my current needs, adding
some compatible parameters from the literature. I am using the parameter
periodic-molecules = yes
in the mdp file, because if not I have a warning about inconsistent shifts.
As Gromacs could not minimize the structure, I just took a smaller version
of the surface compatible with the cut-off radius, with the idea to minimize
it and then simply replicate it to obtain the large surface I need. Now
Gromacs was able to minimize the small system, but I realized that it was
not taking into account the bonded potentials across boundary conditions. I
did not manage to obtain a topology file by the use of pdb2gmx which
included the bonded potentials across periodic boundary conditions, so I
wrote my own program to generate them. I checked that the missing
interactions were properly added.
I run again the simulation with the right topology file for the small
system, and everything worked. The problem is that, when I replicate the
minimized structure in the x and z directions to obtain the structure I need
(and generating a new topology file with the right bond information,
changing the simulation box size properly, etc), Gromacs still can not
minimize the system, so that it does not 'explode' when I later try to
minimize the system after generating a velocity for every atom, even at very
low temperatures.
I also tried to minimize the original, large simulation box with a proper
topology file, to change the minimization method, the minimization step,
tried different constraints, etc, but without success. I have been working
on this problem for three weeks now and I run out of ideas, can any of you
help? I copy one example of mdp I used.
;constraints = all-bonds
constraints = none
; integration parameters
;integrator = l-bfgs
integrator = cg
;integrator = steep
dt = 0.00
nsteps = 15000
periodic-molecules = yes
; center of mass removal
nstcomm = 10
comm_mode = Linear
; neighbour searching
nstlist = 10
ns_type = grid
pbc = xyz ;periodic boundary conditions in all
directions
rlist = 1.5
; electrostatics
coulombtype = PME
rcoulomb = 1.5
; van der Waals interactions
vdwtype = cut-off
rvdw = 1.5
DispCorr = EnerPres ;tail corrections
; Ewald parameters
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 4
ewald_rtol = 1e-6
optimize_fft = yes
; energy minimization
emtol = 10.0
emstep = 0.01
Thanks
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