[gmx-users] Re: reflecting sphere

Pim Schravendijk schraven at mpip-mainz.mpg.de
Wed Oct 19 10:05:42 CEST 2005

> > From: Wang Zhun <wangzhun76 at gmail.com>
> > Hi, Dr Spoel,
> > I wonder if a reflecting sphere can be created by Gromacs. In  PNAS
> > 2004,101(35):12916-12921, Charmm was used to created a reflecting
> > sphere to restrict the interaction simulation between 2 peptide
> > chains. Can gromacs do the same job?
>. You could do the same by calculating the resulting force and
> adding this to the force array. Put it in gmx/src/kernel/md.c, for example
> just before the AFM and Umbrella type pulling is called. It needs the x
> coordinates from the "state->x"  array, and the calculated force should be
> added per atom to the "f" array.  If you define the center of the sphere
> in 0,0,0 and since you don't use PBC, you probably don't need to know the
> box coordinates. The only tricky bit is that you should give the direction
> of the force along the local normal of the spherical surface.

Actually even this last part is simple since you can always work from 
(0,0,0), so the vector on which the force acts is always in the direction 
of the vector connecting your atom with (0,0,0).

Greetings, Pim

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