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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 and r_2). <br>I did not understand very well your last suggestion: "...if you want reasonable error bars you will not lots of well-converged data". <br>Do you mean I will need also more windows besides extending the simulations?<br>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...<br>Thanks a lot again for your help.<br>Best wishes,<br>Rebeca.<br>
<pre><br></pre><br><div><hr id="stopSpelling">From: firstname.lastname@example.org<br>To: email@example.com<br>Date: Thu, 21 Jul 2011 16:36:59 +0000<br>Subject: [gmx-users] large error bars in PMF<br><br>
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</style>Hi,<br><div dir="ltr">I am trying to calculate the binding energy of two molecules using the PMF (Umbrella Sampling method) and Gromacs 4.0.<br>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.<br>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).<br>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. <br>My system has about 29200 atoms (where 29000 are chloroform atoms). The *mdp file I am using is copied below. <br>Would you have any suggestion to improve the results and decrease the 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>                                            </div></div>                                            </div>
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