Hello, I have a quick question on dihedral restraints.
What is the unit of dihre_fc in .mdp file? (It's not on the User's manual) > Add this to your .mdp > ;dihedral restraints > dihre = simple > dihre_fc = 100 ; or whatever value you desire > dihre_tau = 0.0 > nstdihreout = 50 From the test I ran, it seems to be kJ/(mol deg^2 ), but I would like to have confirmation from someone who knows it for sure since I need to calculate exact restraint potential from dihedral angle to calculate PMF profile along dihedral angle. Thank you in advance, Ryogo On Wed, 13 Dec 2006 15:54:28 -0500, [EMAIL PROTECTED] wrote: >> For example, my peptide is rotating 50 degrees about a bond B-C, out >> of four >> bonded atoms A-B-C-D. I want to apply additional force on this >> dihedral(B-C) during my simulation(only for this particular atoms to >> make it >> rotate further till 180 degrees). All the remaining atoms in the peptide >> will have normal force as usual. >> May I ask you, how can I apply this in gromacs code. >> Any help will be appreciated! > > The current manual is good at describing what the options do for > dihedral restraints, but (to my knowlegde) doesn't explain at all how > to get the implementation up and running. Here is how I have done it > based on searching the mailing list for answers. I suggest that > something like this is added by way of example to the manual for > future releases. > > Also, the manual is a bit unclear about whether this type of dihedral > restraint is stable for use near 180deg. I have found that for my > system everything appears to behave normally and as expected over the > entire range of dihedral angles including 180deg. > > In your .top file: > > ; Include forcefield parameters > #include "ffoplsaa.itp" > ; Include topologies > #include "myprotein.itp" > [ dihedral_restraints ] > ; ai aj ak al type label phi dphi kfac power > A B C D 1 1 180 0 1 2 > #include "tip4p.itp" > etc... > Make sure that the dihedral_restraints section comes immediately > after the inclusion of the protein topology. If you have the protein > topology directly in your .top file then just include > dihedral_restraints after the protein listing but before any mention > of things that are not that protein molecule. > > Add this to your .mdp > ;dihedral restraints > dihre = simple > dihre_fc = 100 ; or whatever value you desire > dihre_tau = 0.0 > nstdihreout = 50 > > For more information about what these options mean, please refer to > the manual. > > > > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use thewww > interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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/mailing_lists/users.php
