Re: [gmx-users] MnO2 periodic system

[Dallas Warren]

What do you mean "deformed"?

The "deformation" that you have encountered is probably most likely
due to the topology, rather than the simulation settings (since you
have constant volume set).  So that means there are issues with your
topology.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a nail.


On 5 August 2017 at 02:51, gangotri dey  wrote:
> Dear all,
>
> I am trying to equilibrate a MnO2 surface (not cluster periodic). 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  = 5 ; 2 * 50 = 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= 18; generate a random seed
>
>
>
> *Thank you*
>
> *Gangotri Dey*
> --
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[gmx-users] MnO2 periodic system

[gangotri dey]

Dear all,

I am trying to equilibrate a MnO2 surface (not cluster periodic). 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  = 5 ; 2 * 50 = 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= 18; generate a random seed



*Thank you*

*Gangotri Dey*
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