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OK,<br>I will try a dodecahedral box and also to extend my actual simulations.<br>Could you give me some advice about starting to learn about 3D PMF? I have not seen this in the manual, and I have never used it before. I have only found your tutorial about how to calculate PMF in Gromacs 4...<br>Thanks a lot again for your help.<br>Best wishes,<br>Rebeca.<br><br><div>> Date: Thu, 21 Jul 2011 15:16:52 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: FW: [gmx-users] large error bars in PMF<br>> <br>> <br>> <br>> Rebeca García Fandiño wrote:<br>> > <br>> > <br>> > I am trying to achieve the binding energy of the dimer composed by the <br>> > two small cyclic peptides, to compare it with experimental. What <br>> > advantages would I have using 3D PMF instead only 1D for this calculation?<br>> <br>> Intuitively, two molecules diffuse through solution until they find one another, <br>> which to me sounds a lot like a 3D path. Further, using a dodecahedral box for <br>> your umbrella sampling removes the problems you're having with the peptides <br>> rotating. It sounds like you're trying to pull in one direction along a <br>> rectangular box, but the peptides are not playing nice. I feel like this <br>> discussion has come up at least once or twice before, though...<br>> <br>> -Justin<br>> <br>> > Thanks a lot!<br>> > Rebeca.<br>> > <br>> > > Date: Thu, 21 Jul 2011 14:14:44 -0400<br>> > > From: jalemkul@vt.edu<br>> > > To: gmx-users@gromacs.org<br>> > > Subject: Re: [gmx-users] large error bars in PMF<br>> > ><br>> > ><br>> > ><br>> > > Rebeca García Fandiño wrote:<br>> > > > Hi,<br>> > > > thanks a lot for your quick answer.<br>> > > > What I am trying to pull are two small peptides one from another (r_1<br>> > > > and r_2).<br>> > > > I did not understand very well your last suggestion: "...if you want<br>> > > > reasonable error bars you will not lots of well-converged data".<br>> > ><br>> > > Oops, that should have read "you will *need* lots of well-converged <br>> > data."<br>> > ><br>> > > > Do you mean I will need also more windows besides extending the <br>> > simulations?<br>> > ><br>> > > I doubt you need more windows. Likely you just need more time in each.<br>> > ><br>> > > > I think the problem could be also that the peptides I am using <br>> > rotate in<br>> > > > the box and they do not remain flat one respect to the other. They<br>> > > > gyrate freely and some parts of their structure interact along the<br>> > > > pulling...<br>> > ><br>> > > Interactions are part of the dissociation process and are not <br>> > problematic per<br>> > > se. But if you're trying to obtain only a one-dimensional PMF then your<br>> > > rotation could be a problem. Is there some reason you need a <br>> > one-dimensional<br>> > > PMF and not a three-dimensional PMF? What are you trying to achieve?<br>> > ><br>> > > -Justin<br>> > ><br>> > > > Thanks a lot again for your help.<br>> > > > Best wishes,<br>> > > > Rebeca.<br>> > > ><br>> > > ><br>> > > ><br>> > > > <br>> > ------------------------------------------------------------------------<br>> > > > From: regafan@hotmail.com<br>> > > > To: gmx-users@gromacs.org<br>> > > > Date: Thu, 21 Jul 2011 16:36:59 +0000<br>> > > > Subject: [gmx-users] large error bars in PMF<br>> > > ><br>> > > ><br>> > > > Hi,<br>> > > > I am trying to calculate the binding energy of two molecules using the<br>> > > > PMF (Umbrella Sampling method) and Gromacs 4.0.<br>> > > > Some weeks ago I have written to the list because changing the <br>> > number of<br>> > > > windows used in the Umbrella Sampling calculations different results<br>> > > > were obtained, and I was suggested to extend my simulations since the<br>> > > > error bars associated to each windows were too high.<br>> > > > I have now extended my simulations from 1 ns to 8 ns, however, I <br>> > cannot<br>> > > > see much different from the shorter calculations. I send you the<br>> > > > comparison of the two PMF including the error bars (attached).<br>> > > > Now I am using 50 windows, but the shorter simulations were done using<br>> > > > 100 windows, so I don't think increasing the number of windows <br>> > could help.<br>> > > > My system has about 29200 atoms (where 29000 are chloroform atoms). <br>> > The<br>> > > > *mdp file I am using is copied below.<br>> > > > Would you have any suggestion to improve the results and decrease the<br>> > > > error bars in the calculations?<br>> > > ><br>> > > > ----------------------------MDP file---------------------------<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 ; every 10 ps<br>> > > > nstvout = 5000<br>> > > > nstfout = 5000<br>> > > > nstxtcout = 5000 ; every 10 ps<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 = ACH 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>> > > > -----------------------------------------------<br>> > > ><br>> > > ><br>> > > > Thanks a lot in advance.<br>> > > ><br>> > > > Best wishes,<br>> > > ><br>> > > > Dr. Rebeca Garcia<br>> > > > Santiago de Compostela University<br>> > > > Spain<br>> > > ><br>> > > ><br>> > > ><br>> > > > -- gmx-users mailing list gmx-users@gromacs.org<br>> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the<br>> > > > archive at http://www.gromacs.org/Support/Mailing_Lists/Search before<br>> > > > posting! Please don't post (un)subscribe requests to the list. Use the<br>> > > > www interface or send it to gmx-users-request@gromacs.org. Can't post?<br>> > > > Read http://www.gromacs.org/Support/Mailing_Lists<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 <br>> > 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>> > <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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