Dear All: I am using gromacs4.5.3 to do umbrella sampling simulation of the residue side chain dihedrals. I used the dihedral restrain method described in the mannual to restrain the dihedral values. The method we used is described as follows: ____________________________________________ we first added the following parameters in the *.top file immediately after the parameters of the protein:
[ dihedral_restraints ] ; ai aj ak al type label phi dphi kfac power 4 6 9 12 1 1 180 0 1 2 Then we added the following parameters in the *.mdp file : ; dihedral restraints dihre = yes dihre_fc = 1000 ; or whatever value you desire dihre_tau = 0.0 nstdihreout = 50 _____________________________________________ Then we used the following commond to generate the tpr file: grompp -f ourfile.mdp -c ourfile.gro -p ourfile.top -o ourfile.tpr After the simulations, we used the g_angle commond to calculate the distribution of the dihedral angels: g_angle_d -f oufile.trr -n ourfile.ndx -od ourfile.xvg -type dihedral However, we found that in the simulation results, the dihedral was not restrained as we expected. The dihedral angles distrbuted in a wide range around its initial values and when larger force constant were applied the distribution was not affected. It seemed that the externial forces we assigned was not applied on the residue. The other parameters we used was the same with that we used in un-restrained simulations. Could anyone help me with this problem? Did I used the wrong parameters or are there any other wrong in my simulations? Thanks in advance. Best Regards r.x.g. -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
