[gmx-users] Energy minimization of solvated MOFs.

Dallas Warren dallas.warren at monash.edu
Wed Jul 11 06:27:22 CEST 2018

Have you visualised the system to see what it is about that water that
is generating such a high force?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Wed, 11 Jul 2018 at 00:57, Nagasree Garapati
<nagasree.garapati at mail.wvu.edu> wrote:
> Hi
> 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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