[gmx-users] Steepest Descents converged to machine precision in XX steps
felipe.merino at mpi-dortmund.mpg.de
Tue Mar 7 15:47:45 CET 2017
Sometimes I was able to solve these heavy clashes by minimizing using a
double precision gromacs. Just be sure to heavily constraint the protein
so it does not deform due to the bad starting system geometry.
On 07/03/17 15:11, Justin Lemkul wrote:
> On 3/7/17 9:00 AM, Nikhil Maroli wrote:
>> Dear Justine,
>> My simulation system is a protein on the surface of the lipid layers,
>> is created using charmm-gui. There are no overlapping between atoms or
>> whatsoever. How can i overcome this issue?
> Start by visualizing the system right where mdrun is telling you there
> is an issue. It prints out which atom has the infinite force. That's
> usually a clue.
>> I have remodelled the system by keeping more distance between protein
>> lipids and that time maximum force on atoms came to be 4E18.
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