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{font-size:10pt;font-family:Tahoma</style>I am trying to achieve the binding energy of the dimer composed by the two small cyclic peptides, to compare it with experimental. What advantages would I have using 3D PMF instead only 1D for this calculation?<br><div dir="ltr">Thanks a lot!<br>Rebeca.<br><br><div>> 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 data."<br>> <br>> > Do you mean I will need also more windows besides extending the 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 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 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 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>> > 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 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 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 could help.<br>> > My system has about 29200 atoms (where 29000 are chloroform atoms). 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 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></div> </div></body>
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