Thanks for you prompt reply - I'll try that and post back. -SA On Tue, May 31, 2011 at 4:46 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Shay Teaching wrote: > >> Dear gromacs users, >> >> I am trying to pull a ligand out of a cavity of a membrane protein (along >> the Z axis). >> Problem is, that with every pull settings I have tried the ligand gets >> "stuck" on the protein's center of mass. How can I make it go all the was to >> the bulk water? >> It always gets stuck on the COM. And I've tried using both umbrella and >> constant force, so I'm getting the feeling that I'm missing something >> trivial. >> >> Here's an example of one set of pull-parameters I tried: >> -------------------------------> >> pull = constant_force >> pull_geometry = distance >> > > You can only use the distance method if the distance between pull_group0 > and pull_group1 is constantly decreasing or increasing. If you're moving > through a channel, you should use the position method in conjunction with an > appropriate pull_vec1. > > > pull_dim = N N Y >> pull_start = yes ; define initial COM distance > 0 >> >> pull_ngroups = 1 >> pull_group0 = Protein >> > > You probably need a better reference group, i.e. some subset of residues > that forms the entrance or exit from the channel, but you may be able to get > away with this reference group if you using a more appropriate > pull_geometry, as suggested above. > > -Justin > > > pull_group1 = Ligand >> ;pull_rate1 = -0.001 ; 0.01 nm per ps = 10 nm per ns >> pull_k1 = 1000 ; kJ mol^-1 nm^-2 >> <------------------------------ >> >> Can anyone help enlighten me as to what I am doing wrong? >> Thanks, >> -Shay >> >> P.S. >> Using gromacs 4.0.7. >> >> > -- > ======================================== > > 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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