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
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
