Would you also specify in each US window specific residue instead of the whole protein?
Sreven On Mon, Dec 10, 2012 at 2:47 PM, Steven Neumann <s.neuman...@gmail.com> wrote: > On Mon, Dec 10, 2012 at 2:11 PM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >> On 12/10/12 9:01 AM, Steven Neumann wrote: >>> >>> Dear Gmx Users, >>> >>> I am pulling away cation from the protein glutamic acid residue with: >>> >>> pull = umbrella >>> pull_geometry = distance ; simple distance increase >>> pull_dim = N N Y >>> pull_start = yes ; define initial COM distance > 0 >>> pull_ngroups = 1 >>> pull_group0 = Protein >>> pull_group1 = NA >>> pull_rate1 = 0.01 >>> pull_k1 = 500 ; kJ mol^-1 nm^-2 >>> >>> I tried different pulling rates and simulation time to pull it 3 nm >>> away. I tried pull rate of 0.1; 0.01 and 0.001. The interaction is so >>> strong that the force reaches 600 kJ/mol/nm2 and they do not become >>> separated - with position restraints protein looses its secondary >>> structure and is draged by the ion - they do not become separated. >>> >>> Would you suggest constant force pulling in this case? Then I will >>> extract initial coordinates for US windows. Can I use then US with >>> harmonic potential in windows then and WHAM? >>> >> >> You can generate coordinates in any way you wish. I would think that, >> regardless of the pull method, setting pull_group0 to the actual residue to >> which the ion is coordinated would be significantly more effective than >> pulling with respect to the entire protein, though it seems rather strange >> that the dissociation of an ion would cause a protein to unfold. A stronger >> force constant in pull_k1 may also help. >> >> -Justin > > Thank you Justin. That indeed helped. > > Steven >> >> -- >> ======================================== >> >> Justin A. Lemkul, Ph.D. >> Research Scientist >> 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 -- 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
