Thanks a lot for your quick answer! I think they are separated enough, however my monomers are cyclic (like discs); I start with a parallel conformation between then, but along the Umbrella simulation, both of them rotate and approach. If I do not use restraints, how could I avoid the rotation?
I am using the following md_umbrella.mdp: title = Umbrella pulling simulation define = define = ; Run parameters integrator = md dt = 0.002 tinit = 0 nsteps = 500000 ; 1 ns nstcomm = 10 ; Output parameters nstxout = 5000 nstvout = 5000 nstfout = 5000 nstxtcout = 5000 nstenergy = 5000 ; Bond parameters constraint_algorithm = lincs constraints = all-bonds continuation = yes ; Single-range cutoff scheme nstlist = 5 ns_type = grid rlist = 1.4 rcoulomb = 1.4 rvdw = 1.4 ; PME electrostatics parameters coulombtype = PME fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in two groups Tcoupl = Nose-Hoover tc_grps = r_1_r_2 CL3 tau_t = 0.5 0.5 ref_t = 300 300 ; Pressure coupling is on Pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocities is off gen_vel = no ; Periodic boundary conditions are on in all directions pbc = xyz ; Long-range dispersion correction DispCorr = EnerPres ; Pull code pull = umbrella pull_geometry = distance pull_dim = N N Y pull_start = yes pull_ngroups = 1 pull_group0 = r_1 pull_group1 = r_2 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 Thanks a lot again for your help. Best wishes, Rebeca. > Date: Wed, 22 Jun 2011 10:53:16 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] restraints in PMF (Justin's tutorial) > > > > Rebeca García Fandiño wrote: > > Hello, > > I am trying to obtain the PMF from Umbrella Sampling of the process of > > separating two monomers of a dimer, following Justin 's tutorial > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html > > > > I have done the Umbrella Sampling simulations without using any > > restraints in any of the monomers, however, I can see that they move and > > gyrate so that although the c.o.m are separated from each other, there > > are parts of both interacting, in such way that they are not separated > > as they should be. > > > > Would it be correct if I apply restraints to both monomers in all the > > Umbrella Sampling simulations?. I have seen that in Justin's tutorial > > they applied restraints to one of the chains, but in my case I think I > > will need to restrain both of the units. Would that be correct for the > > PMF calculation? > > > > There are no position restraints applied during the umbrella sampling > simulations. They are unnecessary. The umbrella potential is itself a > restraint to maintain COM separation. > > If parts of your proteins are interacting, you simply haven't fully separated > your monomers and you need to create configurations with greater COM > separation. > If you apply position restraints to fit some notion that your monomers > shouldn't interact at certain distances, then you're applying an unnatural > (and > potentially incorrect) bias, causing the PMF to converge incorrectly. > > -Justin > > > Thanks a lot in advance. > > > > Rebeca. > > > > > Date: Mon, 20 Jun 2011 17:03:56 -0400 > > > From: jalem...@vt.edu > > > To: rega...@hotmail.com > > > CC: gmx-users@gromacs.org > > > Subject: Re: doubt about your Umbrella Sampling tutorial > > > > > > > > > > > > Rebeca García Fandiño wrote: > > > > Dear Justin, > > > > my name is Rebeca and I am a postdoctoral student in Santiago de > > > > Compostela University. Sorry for disturbing you to your personal > > mail, I > > > > have tried to post to the Gromacs-list first, but I did not get any > > answer. > > > > > > I was traveling and not paying much attention to messages across the > > list. I > > > will CC this reply to the list in the hopes that it is useful to > > others, as well. > > > > > > > I am trying to obtain the PMF from Umbrella Sampling of the process of > > > > separating two monomers of a dimer, following your tutorial, and I > > have > > > > a pair of doubts: > > > > > > > > 1)In this tutorial the generation of configurations is done using a > > .mdp > > > > file for pulling one chain from another, but is it possible to > > generate > > > > the configurations for Umbrella Sampling "by hand", I mean, > > changing the > > > > z coordinate of the monomer I want to move, then solvating and then > > > > minimizing these configurations? Is there any problem with this > > protocol > > > > for the obtaining of the configurations? > > > > > > > > > > No problem at all. The tutorial is but one possible method. > > > > > > > 2) I have noticed that you use restraints in the md_umbrella.mdp > > for the > > > > fixed chain. Is that correct? I can understand the restraints in the > > > > pulling simulations for generate starting configurations, but once you > > > > have the configurations, is is necessary to restrain one part of the > > > > system? > > > > > > > > > > Not usually. The tutorial presents a special case. > > > > > > > Thanks a lot in advance for your help with this topic, and thank you > > > > very much also for publishing this interesting tutorial. There was > > > > nothing useful until that for Umbrella Sampling with Gromacs 4.0, so I > > > > think it is more than wellcome for all Gromacs users! > > > > > > Glad they're useful :) > > > > > > -Justin > > > > > > > Best wishes, > > > > Rebeca. > > > > > > > > Dr. Rebeca García Fandiño > > > > Department of Organic Chemistry and Center for Research in Biological > > > > Chemistry > > > > and Molecular Materials > > > > Santiago de Compostela University > > > > E-15782 Santiago de Compostela (Spain) > > > > e-mail: rebeca.garcia.fand...@usc.es > > > > Phone: 34-981563100 ext 15760 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > ======================================== > > > > > > 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 > > > > > > ======================================== > > > > -- > ======================================== > > 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
-- 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
