[gmx-users] Metal organic framework energy minimization

[Lakshman Ji Verma]

Based on these figures it appears that bonds are breaking which means they
are not defined correctly in your topology file.
Based on my experience, you might want to look in your .rtp file and ZIF
gro/pdb file and check the sequence of the atoms. All three files must have
the same sequence of atoms given that bonds are correct defined.

Thanks!
Lakshman

On Wed, Jul 25, 2018 at 2:53 PM Jordan Chapman <jschapman at mix.wvu.edu>
wrote:

> 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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