[gmx-users] Energy minimization of solvated MOFs.

Nagasree Garapati nagasree.garapati at mail.wvu.edu
Tue Jul 10 16:57:42 CEST 2018


I am trying to run some simulations on Metal-Organic frameworks like ZIF-8. I have obtained both structure file (from CCDC) and forcefield data from literature and I was able to successfully run energy minimization, and equilibirum MD (NVT and NPT) simulations on the crystal structure of MOF. But when I tried to perform energy minimization for a system of MOF in water (by putting MOF in a box and solvating using gmx solvate), I am getting following message and forces are very high on water molecules. I am not how to overcome this problem, any thoughts are appreciated.

"Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 5 (which may not be possible for your system). It
stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 95 steps,
but did not reach the requested Fmax < 5.
Potential Energy  = -3.38556029741624e+13
Maximum force     =  2.45386477264935e+25 on atom 306
Norm of force     =  1.49337454338593e+24"

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)

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