Hi again, I have one doub about the suggestion of using a dodecahedral box for my umbrella sampling to remove the problems I am having with the peptides rotating. I cannot see why a dodecaheral box is going to avoid this. Would it be better a truncated octahedron? Thanks a lot 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
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