On Wed, Apr 15, 2015 at 4:39 AM, Agnieszka Slowicka <aslow...@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 > > > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > > http://mackerell.umaryland.edu/~jalemkul > > > > ================================================== > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send > > a mail to gmx-users-requ...@gromacs.org. > > > > > 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 > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
