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

[Mark Abraham]

On Wed, Apr 15, 2015 at 4:39 AM, Agnieszka Slowicka <aslowick at ippt.pan.pl>
wrote:

> >
> >
> > On 4/10/15 12:06 PM, Agnieszka Slowicka wrote:
> >> 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.
> >
> > Given that the energy associated with the dihedral restraints is 0.38
> kJ/mol,
> > I'd say they're just doing very little to help you :)  The dihedral
> restraint
> > options are ignored (well, technically they're removed) in an input .mdp
> file,
> > and it seems that kfac is not a scaling factor at present, it is the
> actual
> > force constant.  That seems to agree with the fact that you're seeing a
> very
> > light restraint with little effect.  Try setting kfac equal to the
> actual
> > force
> > constant you want.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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>
>
> Hi Justin,
>
> Thank you for your suggestions. I introduced kfac=100 in my topology file
> instead of 1 and I think, it's working! So great thank you!!
>
> The dihedral energy reported in .log file is smaller then in the
> simulation calculated with gromacs 4.5.6, but my standard deviation of
> dihedral angles look similar to the restrained in the previous version
> which worked with the old parameters and topology very well.
>
> Do you have any idea why the parameters in the .mdp file are not wrote by
> gromacs 5.0.4? It could be explained in the manual as well, as the form of
> topology files with dihedral restraints.
>

I don't follow. What do you think is not being written by 5.0.4?

Mark


>
> Thank you again,
> Agnieszka
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>
> 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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