[gmx-users] Position restraint doesn't work

asaraujo at if.sc.usp.br asaraujo at if.sc.usp.br
Thu Dec 30 15:03:00 CET 2004

Hi All.

Well... I thought this was a commom problem but I didn't find anything in
I want to perform a simulation in a droplet of acetonitrile to calculate free
The molecules of solvent in the shell of the sphere must to be restrained to not
fly way to the vacuum.
So I changed the resname of these molecules and created another .top file and in
this topology file I included 3 lines of position restraints(only for the
"heavy" atoms C and N):

[ position_restraints ]
   ai   funct   fc
    4      1     1000   1000   1000
    5      1     1000   1000   1000
    6      1     1000   1000   1000

Everything runs fine with grompp and gmxdump (with the lines
functype[XXX]=POSRES in it output), but when I run my simulation the shell
molecules fly away and Warnings like this:

Warning: 1-4 interaction between 1298 and 1303 at distance larger than 5 nm

Came before the simulation crash.
I've already tried to increase de restraint force but it doesn't work.
Can somebody help me?


Alexandre Suman de Araujo


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