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Thanks for your answer.<br>My peptide has 6 residues and it is cyclic.<br>I calculated the errors through bootstrap, using this:<br><br>g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 500 -n Bootstrap 200<br><br>Are the pmfs aligned on the minimum distance value? Is that the value by default? How could I calculate the errors based on the PMFs aligned on the long distance value?<br><br>Thanks a lot for all the help.<br><br>Best wishes,<br><br>Rebeca.<br><br><br><div>> From: x.periole@rug.nl<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] large error bars in PMF<br>> Date: Thu, 21 Jul 2011 14:33:28 -0600<br>> <br>> <br>> One potential problem you have is that as Justin mentioned your minimum<br>> is not well defined and certain much less well sampled than the long <br>> distances<br>> windows. Small peptides (depends the size) may sample relevant phase<br>> space to get reasonable convergence within 8 ns when free in solution;<br>> in contact certainly not ...<br>> <br>> How long is you peptide?<br>> <br>> You might get a better estimate of your error by plotting all the pmfs <br>> you've<br>> got through bootstrap (if this is the case) ... and get the errors <br>> based on the<br>> pmfs aligned on the long distance value and not on the "minimum" which <br>> is<br>> probably what you did ... if the minimum is not well defined then it <br>> does not<br>> make sense.<br>> <br>> On Jul 21, 2011, at 1:36 PM, Justin A. Lemkul wrote:<br>> <br>> ><br>> ><br>> > Rebeca García Fandiño wrote:<br>> >> OK,<br>> >> I will try a dodecahedral box and also to extend my actual <br>> >> simulations.<br>> >> Could you give me some advice about starting to learn about 3D PMF? <br>> >> I have not seen this in the manual, and I have never used it <br>> >> before. I have only found your tutorial about how to calculate PMF <br>> >> in Gromacs 4...<br>> ><br>> > In practice, there's basically nothing different between 3D and 1D. <br>> > You specify the dimensions to which the biasing potential is applied <br>> > with pull_dim or pull_vec (depending on the pull_geometry used). <br>> > Right now you're calculating the PMF along the z-dimension only <br>> > ("pull_dim = N N Y"), which may be appropriate for one-dimensional <br>> > processes or those in which the reference group does not rotate much <br>> > in the timeframe of the sampling. Setting "pull_dim = Y Y Y" will <br>> > apply the restraint in all dimensions.<br>> ><br>> > -Justin<br>> ><br>> >> Thanks a lot again for your help.<br>> >> Best wishes,<br>> >> Rebeca.<br>> >> > 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 <br>> >> 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 <br>> >> calculation?<br>> >> ><br>> >> > Intuitively, two molecules diffuse through solution until they <br>> >> find one another,<br>> >> > which to me sounds a lot like a 3D path. Further, using a <br>> >> dodecahedral box for<br>> >> > your umbrella sampling removes the problems you're having with <br>> >> the peptides<br>> >> > rotating. It sounds like you're trying to pull in one direction <br>> >> along a<br>> >> > rectangular box, but the peptides are not playing nice. I feel <br>> >> 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 <br>> >> another (r_1<br>> >> > > > > and r_2).<br>> >> > > > > I did not understand very well your last suggestion: "...if <br>> >> you want<br>> >> > > > > reasonable error bars you will not lots of well-converged <br>> >> data".<br>> >> > > ><br>> >> > > > Oops, that should have read "you will *need* lots of well- <br>> >> converged<br>> >> > > data."<br>> >> > > ><br>> >> > > > > Do you mean I will need also more windows besides extending <br>> >> the<br>> >> > > simulations?<br>> >> > > ><br>> >> > > > I doubt you need more windows. Likely you just need more time <br>> >> in each.<br>> >> > > ><br>> >> > > > > I think the problem could be also that the peptides I am <br>> >> using<br>> >> > > rotate in<br>> >> > > > > the box and they do not remain flat one respect to the <br>> >> other. They<br>> >> > > > > gyrate freely and some parts of their structure interact <br>> >> 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 <br>> >> 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 <br>> >> achieve?<br>> >> > > ><br>> >> > > > -Justin<br>> >> > > ><br>> >> > > > > Thanks a lot again for your help.<br>> >> > > > > Best wishes,<br>> >> > > > > Rebeca.<br>> >> > > > ><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 <br>> >> molecules using the<br>> >> > > > > PMF (Umbrella Sampling method) and Gromacs 4.0.<br>> >> > > > > Some weeks ago I have written to the list because changing <br>> >> the<br>> >> > > number of<br>> >> > > > > windows used in the Umbrella Sampling calculations <br>> >> different results<br>> >> > > > > were obtained, and I was suggested to extend my simulations <br>> >> 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, <br>> >> however, I<br>> >> > > cannot<br>> >> > > > > see much different from the shorter calculations. I send <br>> >> you the<br>> >> > > > > comparison of the two PMF including the error bars <br>> >> (attached).<br>> >> > > > > Now I am using 50 windows, but the shorter simulations were <br>> >> done using<br>> >> > > > > 100 windows, so I don't think increasing the number of <br>> >> windows<br>> >> > > could help.<br>> >> > > > > My system has about 29200 atoms (where 29000 are chloroform <br>> >> atoms).<br>> >> > > The<br>> >> > > > > *mdp file I am using is copied below.<br>> >> > > > > Would you have any suggestion to improve the results and <br>> >> decrease the<br>> >> > > > > error bars in the calculations?<br>> >> > > > ><br>> >> > > > > ----------------------------MDP <br>> >> 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 <br>> >> search the<br>> >> > > > > archive at http://www.gromacs.org/Support/Mailing_Lists/Search <br>> >> before<br>> >> > > > > posting! Please don't post (un)subscribe requests to the <br>> >> list. Use the<br>> >> > > > > www interface or send it to gmx-users-request@gromacs.org. <br>> >> 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 <br>> >> 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 <br>> >> 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>> > 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 <br>> > before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the www <br>> > 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>> 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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