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

[Smith, Micholas D.]

Alternatively, if the visualization is the only place you don't see the bond (but if you check the topology file and it does show a bond between the metal and the linker is defined) it could be a visualization issue. In that case look at the trjconv command options to center the system and account for the pbc's.

===================
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

________________________________________
From: Smith, Micholas D.
Sent: Tuesday, March 06, 2018 10:52 AM
To: gmx-users at gromacs.org
Subject: Re: Geometry Optimization for Metal organic Frame works

Its the topology generation. It didn't capture that a bond should be where you expected it to be. Bonds will not break in gromacs, so if you are seeing less bonds than you expected its in the topology.


===================
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Nagasree Garapati <nagasree.garapati at mail.wvu.edu>
Sent: Tuesday, March 06, 2018 10:49 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Geometry Optimization for Metal organic Frame works

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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