[gmx-users] Metal organic framework energy minimization

[Jordan Chapman]

Certainly, see the link below. The images should be clearly labeled.
Solvent molecules are hidden for ease of viewing.

https://www.dropbox.com/sh/td7gjj7cwmgsm6m/AAAoSzBdyzh4A7Ij6NTMlnmya?dl=0

Jordan

On Wed, Jul 25, 2018 at 3:08 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> If you can share some links to before and after images on a file sharing
> service, then perhaps someone can suggest what the issue is. I don't follow
> your description so far.
>
> Mark
>
> On Wed, Jul 25, 2018, 15:33 Jordan Chapman <jschapman at mix.wvu.edu> wrote:
>
> > GROMACS users,
> >
> > I am attempting pre-processing of a metal organic framework (ZIF-8) in
> > water, but I am running into trouble with energy minimization. I've added
> > both bonded and nonbonded forcefield parameters for ZIF-8 into the
> AMBER03
> > forcefield library and solvated the system with the TIP3P water model
> using
> > "gmx solvate". The steepest descent algorithm converges to the options I
> > have set in my minimization mdp file, and an analysis of potential energy
> > over the simulation time using "gmx energy" follows an expected trend.
> > However the simulation returns a warning that at several time steps in
> the
> > minimization one or more water molecules could not be settled.
> >
> > Depending on the size of the system I defined using "gmx editconf" I find
> > that the ZIF-8 molecule by the end of the simulation is either crumpled
> > when the box size is too large or stretched to the dimensions of the box
> > when the box size is too small. For reference, the size of a unit cell of
> > ZIF-8 is approximately 1.7 nm x 1.7 nm x 1.7 nm.
> >
> > I've analyzed the range of box dimensions that return either crumpled or
> > stretched ZIF-8 conformations. At a diameter of 3.09 nm, energy
> > minimization returns a stretched ZIF-8 structure. At a diameter of 3.0925
> > nm, energy minimization returns a crumpled ZIF-8 structure. See below for
> > the mdp options I have set for energy minimization. Energy minimization
> of
> > ZIF-8 at the same mdp options was successful for ZIF-8 in vacuum.
> >
> > ; Energy minimization of ZIF-8 unit cell in TIP3P
> > include                  =
> > define                   = -DPOSRES
> >
> > ; RUN CONTROL PARAMETERS
> > integrator               = steep
> > dt                       = 0.001
> > nsteps                   = 100000
> > comm-mode                = Linear
> > nstcomm                  = 20
> > comm-grps                =
> >
> >
> > ; ENERGY MINIMIZATION OPTIONS
> > emtol                    = 10
> > emstep                   = 0.01
> >
> >
> > ; OUTPUT CONTROL OPTIONS
> > nstxout                  = 200
> > nstvout                  = 200
> > nstfout                  = 200
> > nstlog                   = 200
> > nstcalcenergy            = 200
> > nstenergy                = 200
> > nstxout-compressed       = 0
> > energygrps               =
> >
> >
> > ; NEIGHBORSEARCHING PARAMETERS
> > cutoff-scheme            = Verlet
> > nstlist                  = 40
> > ns_type                  = grid
> > pbc                      = xyz
> > periodic-molecules       = yes
> > verlet-buffer-tolerance  = 0.0001
> > rlist                    = 1.4
> >
> >
> > ; OPTIONS FOR ELECTROSTATICS AND VDW
> > coulombtype              = PME
> > coulomb-modifier         =
> > rcoulomb                 = 1.4
> > vdwtype                  = Cut-off
> > vdw-modifier             =
> > rvdw                     = 1.4
> > DispCorr                 = EnerPres
> > ; EWALD/PME/PPPM parameters
> > fourierspacing           = 0.12
> > pme_order                = 4
> > ewald_rtol               = 1e-05
> >
> >
> > ; GENERATE VELOCITIES FOR STARTUP RUN
> > gen-vel                  = no
> > gen-temp                 = 300
> > gen-seed                 = 3532
> >
> >
> > ; OPTIONS FOR BONDS
> > constraints              = none
> >
> > Any advice or insight into what could be causing this or a recommendation
> > for appropriate pre-processing is greatly appreciated!
> >
> > Best,
> > Jordan Chapman
> > Graduate Research Assistant
> > Department of Chemical and Biomedical Enginering
> > West Virginia Univesity
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