[gmx-users] Re: reflecting sphere

Pim Schravendijk schraven at mpip-mainz.mpg.de
Wed Aug 31 01:58:14 CEST 2005

Read the external potential thread here:


I have made a similar adjustment in the gromacs code, but then with walls 
at two ends of the box. I could send you the things I modified, you'd only 
have to change the function a bit to make it a spheric wall. 

You probably could avoid doing this and just use PBC if you had explicit
water instead of continuum solvent, as continuum gives you the unrealistic
ballistic effect they see. If you only need to consider a smaller amount
of water or have access to a good parallel cluster you could always try
that of course :)

> -------- Forwarded Message --------
> From: Wang Zhun <wangzhun76 at gmail.com>
> To: spoel at xray.bmc.uu.se
> Subject: reflecting sphere
> Date: Mon, 29 Aug 2005 18:24:48 +0800
> 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?
> By the way, several posts sent from my email box turned to be
> irregular characters in the mail list. I don't know how this happened,
> because I could receive and read  these my own posts in English in my
> email box.
> Thank you for your help in advance.
> Wang Zhun

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