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

[Felipe Merino]

Hi,

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.

Felipe


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
>>
>