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

Justin A. Lemkul jalemkul at vt.edu
Sat Jan 30 13:18:06 CET 2010

Julian Garrec wrote:
> 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 ?

I don't know what pos0A is doing, but much earlier in the gmxdump output 
should've been something along the lines of:

posres_xA[    0]={ 3.19200e+00,  4.72500e+00,  2.66900e+00}

This line holds the coordinates of each of the restrained atoms.


> Thanks,
> Julian


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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