[gmx-users] Regarding umbrella samplling

Sathish Kumar sathishk238 at gmail.com
Thu Oct 30 06:19:26 CET 2014

Dear gromacs-users,

                         I have run the umbrella sampling with the help of
tutorial of justin. In my system rna is binding with gold nanoparticle. To
find out the binding energy, i run the umbrella sampling using the space
0.1 nm and i got total 79 configurations, each configuration was run for 5
ns. Out of the 79 configurations, only for the 78 and 79 configurations
while running mdrun i am getting the following error.

Fatal error:
Distance of pull group 1 (12.277075 nm) is larger than 0.49 times the box
size (12.526427)

I have used
 pull geometry = distance

How can i solve this problem, please help me in this regard.


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