[gmx-users] Multiple nrexcl commands in GROMACS

[David van der Spoel]

On 2010-08-31 16.23, WJ Evans wrote:
> Hello,
> We are trying to create a model of a carbon nanotube with simple 
> carbon-like chains attached around the entrance and exit of the 
> nanotube. The problem is we need nrexcl set to 3 in nanotube but wnat 
> nrexcl=1 in the chains. We have searched the GROMACS manual and user 
> list extensively and have not found a solution to this issue.
> We would appreciate any advice on how to handle such a modeling situation.
> Thanks you,
> Bill Evans
> Postdoctoral Research Associate
> Rensselaer Polytechnic Inst.
> Nanotechnology Center MRC 275A
> 110 8th St.
> Troy, NY 12180
> 
You can simply generate the exclusions yourself and specify them per
molecule
[ exclusions ]
; From To...
1  2 3 4
2 1 3 4

and so on.

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se