[gmx-users] Metal organic framework energy minimization

[Mark Abraham]

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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