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

[Agnieszka Slowicka]

>
>
> 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.

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

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~