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Thanks a lot for your quick answer!<br>
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.<br>If I do not use restraints, how could I avoid the rotation?<br><br>I am using the following md_umbrella.mdp:<br><br>title = Umbrella pulling simulation<br>define = <br>define =<br>; Run parameters<br>integrator = md<br>dt = 0.002<br>tinit = 0<br>nsteps = 500000 ; 1 ns<br>nstcomm = 10<br>; Output parameters<br>nstxout = 5000 <br>nstvout = 5000<br>nstfout = 5000<br>nstxtcout = 5000 <br>nstenergy = 5000<br>; Bond parameters<br>constraint_algorithm = lincs<br>constraints = all-bonds<br>continuation = yes<br>; Single-range cutoff scheme<br>nstlist = 5<br>ns_type = grid<br>rlist = 1.4<br>rcoulomb = 1.4<br>rvdw = 1.4<br>; PME electrostatics parameters<br>coulombtype = PME<br>fourierspacing = 0.12<br>fourier_nx = 0<br>fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>; Berendsen temperature coupling is on in two groups<br>Tcoupl = Nose-Hoover<br>tc_grps = r_1_r_2 CL3<br>tau_t = 0.5 0.5<br>ref_t = 300 300<br>; Pressure coupling is on<br>Pcoupl = Parrinello-Rahman<br>pcoupltype = isotropic<br>tau_p = 1.0<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Generate velocities is off<br>gen_vel = no<br>; Periodic boundary conditions are on in all directions<br>pbc = xyz<br>; Long-range dispersion correction<br>DispCorr = EnerPres<br>; Pull code<br>pull = umbrella<br>pull_geometry = distance<br>pull_dim = N N Y<br>pull_start = yes<br>pull_ngroups = 1<br>pull_group0 = r_1<br>pull_group1 = r_2<br>pull_init1 = 0<br>pull_rate1 = 0.0<br>pull_k1 = 1000 ; kJ mol^-1 nm^-2<br>pull_nstxout = 1000 ; every 2 ps<br>pull_nstfout = 1000 ; every 2 ps<br><br>Thanks a lot again for your help.<br><br>Best wishes,<br><br>Rebeca.<br><br><div>> Date: Wed, 22 Jun 2011 10:53:16 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] restraints in PMF (Justin's tutorial)<br>> <br>> <br>> <br>> Rebeca García Fandiño wrote:<br>> > Hello,<br>> > I am trying to obtain the PMF from Umbrella Sampling of the process of <br>> > separating two monomers of a dimer, following Justin 's tutorial<br>> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/index.html<br>> > <br>> > I have done the Umbrella Sampling simulations without using any <br>> > restraints in any of the monomers, however, I can see that they move and <br>> > gyrate so that although the c.o.m are separated from each other, there <br>> > are parts of both interacting, in such way that they are not separated <br>> > as they should be.<br>> > <br>> > Would it be correct if I apply restraints to both monomers in all the <br>> > Umbrella Sampling simulations?. I have seen that in Justin's tutorial <br>> > they applied restraints to one of the chains, but in my case I think I <br>> > will need to restrain both of the units. Would that be correct for the <br>> > PMF calculation?<br>> > <br>> <br>> There are no position restraints applied during the umbrella sampling <br>> simulations. They are unnecessary. The umbrella potential is itself a <br>> restraint to maintain COM separation.<br>> <br>> If parts of your proteins are interacting, you simply haven't fully separated <br>> your monomers and you need to create configurations with greater COM separation. <br>> If you apply position restraints to fit some notion that your monomers <br>> shouldn't interact at certain distances, then you're applying an unnatural (and <br>> potentially incorrect) bias, causing the PMF to converge incorrectly.<br>> <br>> -Justin<br>> <br>> > Thanks a lot in advance.<br>> > <br>> > Rebeca.<br>> > <br>> > > Date: Mon, 20 Jun 2011 17:03:56 -0400<br>> > > From: jalemkul@vt.edu<br>> > > To: regafan@hotmail.com<br>> > > CC: gmx-users@gromacs.org<br>> > > Subject: Re: doubt about your Umbrella Sampling tutorial<br>> > ><br>> > ><br>> > ><br>> > > Rebeca García Fandiño wrote:<br>> > > > Dear Justin,<br>> > > > my name is Rebeca and I am a postdoctoral student in Santiago de<br>> > > > Compostela University. Sorry for disturbing you to your personal <br>> > mail, I<br>> > > > have tried to post to the Gromacs-list first, but I did not get any <br>> > answer.<br>> > ><br>> > > I was traveling and not paying much attention to messages across the <br>> > list. I<br>> > > will CC this reply to the list in the hopes that it is useful to <br>> > others, as well.<br>> > ><br>> > > > I am trying to obtain the PMF from Umbrella Sampling of the process of<br>> > > > separating two monomers of a dimer, following your tutorial, and I <br>> > have<br>> > > > a pair of doubts:<br>> > > ><br>> > > > 1)In this tutorial the generation of configurations is done using a <br>> > .mdp<br>> > > > file for pulling one chain from another, but is it possible to <br>> > generate<br>> > > > the configurations for Umbrella Sampling "by hand", I mean, <br>> > changing the<br>> > > > z coordinate of the monomer I want to move, then solvating and then<br>> > > > minimizing these configurations? Is there any problem with this <br>> > protocol<br>> > > > for the obtaining of the configurations?<br>> > > ><br>> > ><br>> > > No problem at all. The tutorial is but one possible method.<br>> > ><br>> > > > 2) I have noticed that you use restraints in the md_umbrella.mdp <br>> > for the<br>> > > > fixed chain. Is that correct? I can understand the restraints in the<br>> > > > pulling simulations for generate starting configurations, but once you<br>> > > > have the configurations, is is necessary to restrain one part of the<br>> > > > system?<br>> > > ><br>> > ><br>> > > Not usually. The tutorial presents a special case.<br>> > ><br>> > > > Thanks a lot in advance for your help with this topic, and thank you<br>> > > > very much also for publishing this interesting tutorial. There was<br>> > > > nothing useful until that for Umbrella Sampling with Gromacs 4.0, so I<br>> > > > think it is more than wellcome for all Gromacs users!<br>> > ><br>> > > Glad they're useful :)<br>> > ><br>> > > -Justin<br>> > ><br>> > > > Best wishes,<br>> > > > Rebeca.<br>> > > ><br>> > > > Dr. Rebeca García Fandiño<br>> > > > Department of Organic Chemistry and Center for Research in Biological<br>> > > > Chemistry<br>> > > > and Molecular Materials<br>> > > > Santiago de Compostela University<br>> > > > E-15782 Santiago de Compostela (Spain)<br>> > > > e-mail: rebeca.garcia.fandino@usc.es<br>> > > > Phone: 34-981563100 ext 15760<br>> > > ><br>> > > ><br>> > > ><br>> > > ><br>> > > ><br>> > > ><br>> > > ><br>> > ><br>> > > --<br>> > > ========================================<br>> > ><br>> > > Justin A. Lemkul<br>> > > Ph.D. Candidate<br>> > > ICTAS Doctoral Scholar<br>> > > MILES-IGERT Trainee<br>> > > Department of Biochemistry<br>> > > Virginia Tech<br>> > > Blacksburg, VA<br>> > > jalemkul[at]vt.edu | (540) 231-9080<br>> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> > ><br>> > > ========================================<br>> > <br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> MILES-IGERT Trainee<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists<br></div> </div></body>
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