OK, I will try to increase the distances of the c.o.m of both molecules to eliminate any contact between them, adding more windows. Thanks a lot for your help! Best wishes, Rebeca.
> Date: Wed, 22 Jun 2011 11:51:36 -0400 > From: [email protected] > To: [email protected] > Subject: Re: [gmx-users] restraints in PMF (Justin's tutorial) > > > > Rebeca García Fandiño wrote: > > 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? > > > > You don't. Why wouldn't two molecules rotate freely in solution when binding > or > unbinding? It seems like completely natural behavior. Even in simple > systems > of protein-ligand association, part of the binding energy is the entropic > restriction of the ligand into a certain binding-competent pose. Why > wouldn't > that happen here? Sounds like an artificial notion to me. > > -Justin > > > 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: [email protected] > > > To: [email protected] > > > 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: [email protected] > > > > > To: [email protected] > > > > > CC: [email protected] > > > > > 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: [email protected] > > > > > > 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 [email protected] > > > 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 [email protected]. > > > 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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