I did not quite understand your comment.
However, I am trying my best to answer it.
I have a surface MnO2 model. I have solvated the structure in all 3
directions. After that, I minimize it and run NVT simulation with the
parameters as mentioned. However, I see that there is a deformation of the
surface and it does not remain a flat surface. Instead, it curls like a
ribbon. This should not be the case. Hence, I am wondering what are the
factors that can lead to this deformation? Are the parameters in the NVT
simulation good enough or else there is a problem that I cannot see.
G
There are a few points to be made...
1. The shape of your system, which is "solvated in all 3 directions" is
very unclear. Is this a brick floating in water?
2. Please do not solvate anything until you have established that your
"surface" is happy in vacuum.
3. If you have bending as a whole, it could be indicative of large
internal strains, in which case NVT is probably a poor option. When you
say you have "a surface MnO2 model," is it something like this?
https://upload.wikimedia.org/wikipedia/commons/8/81/Manganese-dioxide-from-xtal-sheet-3D-balls.png
4. This community is mostly focused on biomolecular simulations and
noone will be able to verify your parameterization of a solid crystal.
Here is the rule of thumb though: If something bends when it shouldn't
bend, your model is bad, which really has nothing to do with Gromacs.
5. If you are a student and points 1-4 aren't something your doctoral
advisor already mentioned, maybe you should find another advisor.
Alex
Hi,
Are you trying to implement a model that you know is capable of produce a
surface that does not deform in unexpected ways?
Mark
On Mon, 7 Aug 2017 16:35 gangotri dey <holyriv...@gmail.com> wrote:
Dear all,
I am trying to equilibrate a MnO2 surface (not cluster but periodic). I
have solvated the surface with water in all 3 directions. After the NVT
run, I see that the surface is deformed. I was wondering what else can
I
add in my nvt.mdp to not encounter this problem?
I have mainly followed the examples in the forum for graphene/CNT
growth.
title = MnO2 in H2O NVT equilibration
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 500000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 50 ; save coordinates every 0.10 ps
nstvout = 50 ; save velocities every 0.10 ps
nstenergy = 50 ; save energies every 0.10 ps
nstlog = 50 ; update log file every 0.10 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = none ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant
with
Verlet
rcoulomb = 1.0 ; short-range electrostatic
cutoff
(in nm)
rvdw = 1.0 ; short-range van der Waals
cutoff
(in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen
thermostat
tc-grps = SOL MnO ; three coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for
each
group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
periodic-molecules = yes
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell
distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = 188888 ; generate a random seed
*Thank you*
*Gangotri Dey*
Postdoctoral Associate
Rutgers University New Brunswick
Chemistry and Chemical Biology
174 Frelinghuysen Road, Piscataway, NJ 08854
Phone: +16092162254
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