Thanks Justin, I think I have the restraints section sorted........... However, once all of the dihedrals are obtained from the MDs, I would like to do a WHAM analysis, of the reaction pathway. As I have to run each conformation as a separate MD in order to obtain all dihedral conformations, how can I do this. g-wham in gmx requires .pdo files from the US output, but since I cannot use US (in the classical sense) for a dihedral, how can i generate a final plot of free energy vrs dihedral??? Thanks again, for all the help, Joanne
On Fri,. Mar 4, 2011 at 1:33 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Joanne Martin wrote: > >> 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?? >> >> > That's controlled in the topology. See the manual, section 4.3.3 and table > 5.6. > > -Justin > > Regards, >> Joanne >> >> >> On Fri, Mar 4, 2011 at 1:09 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> 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 <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > 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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