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
