Thanks for your answer. My peptide has 6 residues and it is cyclic. I calculated the errors through bootstrap, using this:
g_wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal -b 500 -n Bootstrap 200 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? Thanks a lot for all the help. Best wishes, Rebeca. > From: x.peri...@rug.nl > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] large error bars in PMF > Date: Thu, 21 Jul 2011 14:33:28 -0600 > > > One potential problem you have is that as Justin mentioned your minimum > is not well defined and certain much less well sampled than the long > distances > windows. Small peptides (depends the size) may sample relevant phase > space to get reasonable convergence within 8 ns when free in solution; > in contact certainly not ... > > How long is you peptide? > > You might get a better estimate of your error by plotting all the pmfs > you've > got through bootstrap (if this is the case) ... and get the errors > based on the > pmfs aligned on the long distance value and not on the "minimum" which > is > probably what you did ... if the minimum is not well defined then it > does not > make sense. > > On Jul 21, 2011, at 1:36 PM, Justin A. Lemkul wrote: > > > > > > > Rebeca García Fandiño wrote: > >> OK, > >> I will try a dodecahedral box and also to extend my actual > >> simulations. > >> 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... > > > > In practice, there's basically nothing different between 3D and 1D. > > You specify the dimensions to which the biasing potential is applied > > with pull_dim or pull_vec (depending on the pull_geometry used). > > Right now you're calculating the PMF along the z-dimension only > > ("pull_dim = N N Y"), which may be appropriate for one-dimensional > > processes or those in which the reference group does not rotate much > > in the timeframe of the sampling. Setting "pull_dim = Y Y Y" will > > apply the restraint in all dimensions. > > > > -Justin > > > >> Thanks a lot again for your help. > >> Best wishes, > >> Rebeca. > >> > Date: Thu, 21 Jul 2011 15:16:52 -0400 > >> > From: jalem...@vt.edu > >> > To: gmx-users@gromacs.org > >> > Subject: Re: FW: [gmx-users] large error bars in PMF > >> > > >> > > >> > > >> > Rebeca García Fandiño wrote: > >> > > > >> > > > >> > > 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? > >> > > >> > Intuitively, two molecules diffuse through solution until they > >> find one another, > >> > which to me sounds a lot like a 3D path. Further, using a > >> dodecahedral box for > >> > your umbrella sampling removes the problems you're having with > >> the peptides > >> > rotating. It sounds like you're trying to pull in one direction > >> along a > >> > rectangular box, but the peptides are not playing nice. I feel > >> like this > >> > discussion has come up at least once or twice before, though... > >> > > >> > -Justin > >> > > >> > > Thanks a lot! > >> > > Rebeca. > >> > > > >> > > > Date: Thu, 21 Jul 2011 14:14:44 -0400 > >> > > > From: jalem...@vt.edu > >> > > > To: gmx-users@gromacs.org > >> > > > Subject: Re: [gmx-users] large error bars in PMF > >> > > > > >> > > > > >> > > > > >> > > > Rebeca García Fandiño wrote: > >> > > > > Hi, > >> > > > > thanks a lot for your quick answer. > >> > > > > What I am trying to pull are two small peptides one from > >> another (r_1 > >> > > > > and r_2). > >> > > > > I did not understand very well your last suggestion: "...if > >> you want > >> > > > > reasonable error bars you will not lots of well-converged > >> data". > >> > > > > >> > > > Oops, that should have read "you will *need* lots of well- > >> converged > >> > > data." > >> > > > > >> > > > > Do you mean I will need also more windows besides extending > >> the > >> > > simulations? > >> > > > > >> > > > I doubt you need more windows. Likely you just need more time > >> in each. > >> > > > > >> > > > > I think the problem could be also that the peptides I am > >> using > >> > > rotate in > >> > > > > the box and they do not remain flat one respect to the > >> other. They > >> > > > > gyrate freely and some parts of their structure interact > >> along the > >> > > > > pulling... > >> > > > > >> > > > Interactions are part of the dissociation process and are not > >> > > problematic per > >> > > > se. But if you're trying to obtain only a one-dimensional PMF > >> then your > >> > > > rotation could be a problem. Is there some reason you need a > >> > > one-dimensional > >> > > > PMF and not a three-dimensional PMF? What are you trying to > >> achieve? > >> > > > > >> > > > -Justin > >> > > > > >> > > > > Thanks a lot again for your help. > >> > > > > Best wishes, > >> > > > > Rebeca. > >> > > > > > >> > > > > > >> > > > > > >> > > > > > >> > > > >> ------------------------------------------------------------------------ > >> > > > > From: rega...@hotmail.com > >> > > > > To: gmx-users@gromacs.org > >> > > > > Date: Thu, 21 Jul 2011 16:36:59 +0000 > >> > > > > Subject: [gmx-users] large error bars in PMF > >> > > > > > >> > > > > > >> > > > > Hi, > >> > > > > I am trying to calculate the binding energy of two > >> molecules using the > >> > > > > PMF (Umbrella Sampling method) and Gromacs 4.0. > >> > > > > Some weeks ago I have written to the list because changing > >> the > >> > > number of > >> > > > > windows used in the Umbrella Sampling calculations > >> different results > >> > > > > were obtained, and I was suggested to extend my simulations > >> since the > >> > > > > error bars associated to each windows were too high. > >> > > > > I have now extended my simulations from 1 ns to 8 ns, > >> however, I > >> > > cannot > >> > > > > see much different from the shorter calculations. I send > >> you the > >> > > > > comparison of the two PMF including the error bars > >> (attached). > >> > > > > Now I am using 50 windows, but the shorter simulations were > >> done using > >> > > > > 100 windows, so I don't think increasing the number of > >> windows > >> > > could help. > >> > > > > My system has about 29200 atoms (where 29000 are chloroform > >> atoms). > >> > > The > >> > > > > *mdp file I am using is copied below. > >> > > > > Would you have any suggestion to improve the results and > >> decrease the > >> > > > > error bars in the calculations? > >> > > > > > >> > > > > ----------------------------MDP > >> file--------------------------- > >> > > > > 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 ; every 10 ps > >> > > > > nstvout = 5000 > >> > > > > nstfout = 5000 > >> > > > > nstxtcout = 5000 ; every 10 ps > >> > > > > 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 = ACH 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 in advance. > >> > > > > > >> > > > > Best wishes, > >> > > > > > >> > > > > Dr. Rebeca Garcia > >> > > > > Santiago de Compostela University > >> > > > > Spain > >> > > > > > >> > > > > > >> > > > > > >> > > > > -- gmx-users mailing list gmx-users@gromacs.org > >> > > > > 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 gmx-users-requ...@gromacs.org. > >> 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 gmx-users@gromacs.org > >> > > > 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 gmx-users-requ...@gromacs.org. > >> > > > 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 gmx-users@gromacs.org > >> > 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 gmx-users-requ...@gromacs.org. > >> > 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 gmx-users@gromacs.org > > 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 gmx-users-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > -- > gmx-users mailing list gmx-users@gromacs.org > 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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists