[gmx-users] Including a position restraint file

[Yang Ye]

Bob Johnson wrote:

>Hello everyone,
>I am trying to include a restraint file in my simulation. Here's a copy of my
>topology file
>
>; Biosensor
>
>;Include force field files
>#include "ffbiosensor.itp"
>
>;Include molecule topologies
>#include "cnt_26_0.itp"            ;nanotube topology
>  
>
;Position restraints on nanotube

#ifdef POSRES_NANOTUBE
#include "posre_nanotube.itp"
#endif

>#include "ssdna_nopairs.itp"       ;ssdna topology
>#include "water.itp"               ;water topology
>
[ system ]

>;Name
>Biosensor
>
>[ molecules ]
>;Molecule name          Number of molecules
>cnt_26_0                1
>ssdna                   1
>water                   124
>
>Grompp gives errors when I have the include statement in the position as shown.
>It says:
>Fatal error: [ file "posre_nanotube.itp", line 8 ]:
>Atom index (4) in position_restraints out of bounds (1-3)
>  
>
You were actually putting the restraints on the water.

>I have 2080 atoms in my nanotube. Where do I put the include statement?
>Thanks,
>Bob Johnson
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>  
>