[gmx-users] Steepest Descents converged to machine precision in XX steps

Felipe Merino 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, 
>> which
>> 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.
> -Justin
>> I have remodelled the system by keeping more distance between protein 
>> and
>> lipids and that time maximum force on atoms came to be 4E18.
>> Thanks

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