[gmx-users] error in Umbrella sampling

[John Whittaker]

Hi,

Without any information about the parameters you are using in your
simulation, no one will be able to provide much help.

I recommend reading and understanding this tutorial before you try to
perform an umbrella simulation totally blind:

http://www.mdtutorials.com/gmx/umbrella/index.html

The error is exactly what it says it is. The distance between your pull
groups cannot be larger than 0.49 times the box size in one of the
dimensions you are pulling because Gromacs calculates the pull distance
taking periodic boundary conditions into account. Therefore, if you pull
farther than half the box length, the COM distance will be calculated
between one of your groups in the simulation box and a group's periodic
image in the adjacent periodic cell... and that distance no longer makes
any physical sense.

This and more are explained in the link given above.

Best,

John

> Dear all,,
>               I am performing Umbrella sampling on a beeta-sheet to
> determine the binding energy between them. I got the following error.
> Fatal error:
> Distance between pull groups 1 and 2 (4.908636 nm) is larger than 0.49
> times
> the box size (4.908511).
> while the box-length after equilibratin is
> 9.99217   3.99687   5.99530
> I am doing umbrella sampling for the first time. Therefore, I am not able
> to understand the error thrown by mdrun. Any help will be appreciated.
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