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

Momin Ahmad momin.ahmad at kit.edu
Wed Mar 7 16:05:27 CET 2018


i am also simulating MOFs with gromacs and can say that OBGMX is not the 
best way to generate the topology file. It has many flaws but shows some 
ideas. I am currently creating my own forcefield using the UFF4MOF by M. 
Addicoat. You can have a look at it:



Am 07.03.2018 um 14:25 schrieb Nagasree Garapati:
> Thank You Micholas
> I have created the topology files using initial input file in OBGMX and it shows that there are 20 unique bond terms, out of which there are 3 bonds between the metal ion and the N2 in linker.
> However, when I tried to create topolgies using the optimized final output (final.gro) file in OBGMX, nothing is created I have empty files for both .top and .itp files.
> I believe there is something wrong with the topology files, but I am not able to figure out where is the mistake.
> Any suggestions ?
> Thank You
> 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)

Momin Ahmad

Karlsruhe Institute of Technology (KIT)
Steinbuch Centre for Computing (SCC)
Hermann-von-Helmholtz-Platz 1
76344 Eggenstein-Leopoldshafen
Phone: +49 721 608-24286
E-Mail: Momin.Ahmad at kit.edu

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