[gmx-users] Geometry Optimization for Metal organic Frame works

Nagasree Garapati nagasree.garapati at mail.wvu.edu
Tue Mar 6 16:49:50 CET 2018

Hi All

I am new user for GROMACS and I am trying model Metal Organic Frame works (MOFs)

I have crystal structure (CIF) file downloaded from Cambridge Crystallographic Data Center (CCDC) and used OBGMX tool to develop force field parameters and used following minim.mdp file for optimization. But after optimization, when I visualize the output .gro file I see that all the bonds between the Metal atom and the linker is broken and no.of bonds is less than the original bonds.

Can this be due to the topology file created or am I missing something in mdp file. If anyone has experience with modeling MOFs using GROMACS, I really appreciate your help.

Thank You

; minim.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 75.0  ; Stop minimization when the maximum force < 100.0 kJ/mol/nm
emstep      = 0.1      ; Energy step size
nsteps = 1000   ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist     = 1     ; Frequency to update the neighbor list and long range forces
cutoff-scheme   = Verlet
ns_type     = grid ; Method to determine neighbor list (simple, grid)
coulombtype     = Cut-off ; Treatment of long range electrostatic interactions
rcoulomb     = 2.0 ; Short-range electrostatic cut-off
rvdw     = 2.0 ; Short-range Van der Waals cut-off
rlist     = 2.0 ; Short-range neighbor cut-off
pbc         = xyz ; Periodic Boundary Conditions (yes/no)

With Regards
Nagasree Garapati
Research Assistant Professor
Dept of Chemical and Biomedical Engineering
West Virginia University
PO Box 6102
Morgantown, WV 26506-6102
304 293-5028<tel:304%20293-5028>(O)
304 276-3674(M)

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