[gmx-users] problem with position restraints: X0 set to zero

Julian Garrec julian.garrec at epfl.ch
Sat Jan 30 10:22:31 CET 2010

Dear GROMACS users,

I am trying to equilibrate my system (monomeric protein in water) and I 
want to use position restraint on heavy atoms of the solute using the 
posre.itp file. For some reason, grompp applies correctly the force 
constant I want, but sets all the reference positions to zero. Of course 
I would like this ref. positions to be taken from my .gro file:

${GROMPP} -debug 10 -f inp.mdp -po out.mdp -c first.gro -r first.gro -p 
prm.top -o allprm.tpr -maxwarn 10

Here are the first line of my posre.itp file:

[ position_restraints ]
; atom  type      fx      fy      fz
     1     1 567 567 567

... and the first line containing the "POSRES" flag in my tpr file 
(dumped with gmxdump):

functype[441]=POSRES, pos0A=( 0.00000000e+00, 0.00000000e+00, 
0.00000000e+00), fcA=( 5.67000000e+02, 5.67000000e+02, 5.67000000e+02), 
pos0B=( 0.00000000e+00, 0.00000000e+00, 0.00000000e+00), fcB=( 
5.67000000e+02, 5.67000000e+02, 5.67000000e+02)

Using the -debug option with grompp didn't provide me further information.

Does anybody know how to cure this problem ?



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