[gmx-users] Regarding umbrella samplling

Justin Lemkul jalemkul at vt.edu
Thu Oct 30 13:01:05 CET 2014

On 10/30/14 1:19 AM, Sathish Kumar wrote:
> 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.

As described in the tutorial, the pulled distance (when using geometry = 
distance) cannot exceed half of the box size due to issues related to 
periodicity of the system.  You'll have to decide whether or not you need to be 
pulling this far, but if you do, you need to set up a larger box.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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