Hi Justin, thanks so much for the swift reply. With regards to the mdp setting
> The proper setting for the "dihre" keyword is either "yes" or "no." How to I specify which dihedral I want to restrain and the force constant which I want to apply to it?? Regards, Joanne On Fri, Mar 4, 2011 at 1:09 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Joanne Martin wrote: > >> Hi, I'm a trying to calculate the PMF of a dihedral using Gromacs version >> 4.04. >> I have read through all posts on the mailing list regarding this query, >> and although Chris Neale did explain how to set the restraints for Gromacs >> 3, these options are now obsolete for 4.04............ I get the following >> error > >> >> Ignoring obsolete mdp entry 'domain-decomposition' >> Replacing old mdp entry 'unconstrained-start' by 'continuation' >> Ignoring obsolete mdp entry 'dihre_tau' >> Ignoring obsolete mdp entry 'nstdihreout' >> Ignoring obsolete mdp entry 'nstcheckpoint' >> ERROR: invalid enum 'simple' for variable dihre, using 'no' >> >> > The proper setting for the "dihre" keyword is either "yes" or "no." > > > I have read Chris's paper from 2008 on alanine dihedrals but again this is >> done using Gromacs 3, and his tutorial for US in based on distance >> restraints. >> >> Basically I have two conformations of a sugar ( a starting conformation >> and an end conformation), and I want to generate a series of snapshots ie a >> reaction coordinate, from a "pulled" MD, for use in US. >> The pull code is only applicable to distance restraints, so how can I >> apply a restraint to the dihedral so that it will sample all dihedrals from >> the initial -180deg through to the end +180deg? >> >> > You need to generate any intermediate structures at angles you wish to > sample. There is no mechanism to enforce the rotation about a dihedral > presently implemented in Gromacs. > > > I would really appreciate if someone could explain to me, where I should >> set the restraints, as this is not clear from the manual. >> Also once the initial configurations are generated, is the below mdp >> option accurate for US of a dihedral > >> (query regarding distance option should this be direction??) >> > > The pull code is irrelevant here. Please do not attempt to apply my > tutorial to your problem (beyond basic theory), as you will probably only > frustrate yourself by doing so. > > When using a dihedral restraint, an energy term corresponding to the > restraint should be written to the .edr file. I imagine you can plot these > values as a function of the dihedral angle to extract the information you > want. > > -Justin > > > >> ; Pull code >> pull = umbrella >> pull_geometry = *_distance_* ; can't get PMF with direction >> >> >> pull_dim = N N Y >> pull_start = yes pull_ngroups = 1 >> pull_group0 = ? pull_group1 = ? >> pull_init1 = 0 >> pull_rate1 = 0.0 >> pull_k1 = 1000 ; kJ mol^-1 nm^-2 >> pull_nstxout = 1000 ; every 2 ps >> pull_nstfout = 1000 ; every 2 ps >> >> >> >> >> Can someone please get back to me with any suggestions you may have, >> >> >> Kindest regards, >> Joanne >> >> >> >> >> >> >> >> >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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