[gmx-users] Metal organic framework energy minimization

[Lakshman Ji Verma]

On Wed, Jul 25, 2018 at 8:32 AM 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.
>

I have come across these errors. Apparently in my cases, water atoms
overlap with the other molecule. It happens because when we add water
molecules with gmx solvate, water molecules are added in all the possible
vacant spaces and some water molecules are added within molecules where
they are not supposed to be. So, I think water molecules in your case are
being inserted within the ZIF-8 framework where there is not enough space.
You might want to look at your input .gro file for minimization and remove
those water molecules.



> 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.
>

If bonds are breaking. You might want to look at bonds and dihedral angles
in your topology file and see if all the atoms are  connected correctly.

Thanks!
Lakshman


> 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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>