[gmx-users] problem with dihedral restraints in gromacs 5.0.4

[Agnieszka Slowicka]

Hello,

I have a problem with implementation of dihedral restraints in gromacs 5.0.4.

I introduced restraints into a topology file after the section with
protein topology as fallowing:

; dihedral restraints added manually: phi,psi, chi1 and chi2
; reference values = cluster 1 of charmm/tip4p
[ dihedral_restraints ]
; ai   aj    ak    al     type  phi  dphi  kfac
; phi C(n-1) - N - CA - C
    5    7     9    29     1    -82     0     1
; psi N - CA - C - N(n+1)
    7    9    29    30     1     121    0     1
; chi1 N - CA - CB - CG
    7    9    11    14     1    -177    0     1
; chi1 CA - CB - CG - CD1
    9    11    14     15   1    -106    0     1

The previous version of the topology file with label and power parameters
doesn't work generating error.

I introduced the restraints section into the .mdp:

;dihedral restraints
dihre               =  yes
dihre_fc            =  100     ; kJ/(mol rad^2)
dihre_tau           =  0.0
nstdihreout         =  250


Gromacs works with this implementation but the restraints are not take
into account. I don't see information about input parameters for dihedral
restraints in my log file, however something is calculated because I found
there:

Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.          LJ-14
    1.71840e+01    6.93870e+01    4.03491e+01    7.20053e+00    4.07828e+01
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.     Dih. Rest.
    1.80019e+02    6.68397e+03   -4.46824e+04    1.08339e+02    3.82359e-01
      Potential    Kinetic En.   Total Energy  Conserved En.    Temperature


I am sure that my restraints don't work because standard deviation of
restrained angles is the same order like without restraints.

Could you help me with this problem?

Regards,

Agnieszka Slowicka

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Agnieszka M. Slowicka
Department of Fluid Dynamics
Institute of Fundamental Technological Research,
Polish Academy of Sciences,
ul.Pawinskiego 5b, 02-106 Warsaw, Poland
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