[gmx-users] dihedral

[Francesco Oteri]

Dear gromacs users,
I'm trying to restrain the value of a particular dihedral using the 
section "[ dihedral_restraints ]" :

[ dihedral_restraints ]
  ; ai             aj        ak        al    type    label       
phi      dphi kfac power
  13919 13915 13921 13922    1          1      -67.19       0     1    4

I ran an energy minimization through
mdrun_d -deffnm 01em -v -debug 6

but, unfortunately, the values are far from the wanted value ( in 
radians -67.19 = -1.17)  as grep reveals:

grep dihres mdrun_d.debug
dihres[0]: 12650 12647 12651 12652 : phi=-1.090441, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12650 12647 12651 12652 : phi=-1.090497, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12650 12647 12651 12652 : phi=-1.090586, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12650 12647 12651 12652 : phi=-1.090734, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12650 12647 12651 12652 : phi=-1.090996, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12650 12647 12651 12652 : phi=-1.091487, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12650 12647 12651 12652 : phi=-1.092475, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12650 12647 12651 12652 : phi=-1.094620, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12650 12647 12651 12652 : phi=-1.099689, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12650 12647 12651 12652 : phi=-1.112823, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12650 12647 12651 12652 : phi=-1.147934, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12650 12647 12651 12652 : phi=-1.230998, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12650 12647 12651 12652 : phi=-0.342237, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12650 12647 12651 12652 : phi=-1.931253, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12650 12647 12651 12652 : phi=1.093490, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12650 12647 12651 12652 : phi=-0.846042, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12650 12647 12651 12652 : phi=1.893053, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12649 12646 12650 12651 : phi=-0.523006, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12649 12646 12650 12651 : phi=2.245932, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12649 12646 12650 12651 : phi=-1.518727, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12649 12646 12650 12651 : phi=1.665189, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12648 12645 12649 12650 : phi=-1.820232, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12648 12645 12649 12650 : phi=1.414995, dphi=0.000000, 
kfac=100.000000, power=4, label=1
dihres[0]: 12648 12645 12649 12650 : phi=-2.154156, dphi=0.000000, 
kfac=100.000000, power=4, label=1

Do I made any error or did I miss something?

The .top, .pdb and .mdp files to reproduce my problem can be downloaded 
from http://160.80.35.105/download/
Since there are same not-standard residues, I've attacched the file 
obtained using the option -pp in grompp.


Francesco