余翔 wrote: > Dear all: > > I have a problem when I was running mdrun on different computers. I > made a .tpr file including coordinate and velocity of each atom from a crash > of mdrun and upload it to four computers whose distribution version of linux > and gcc were as follows: > computer A: Redhat 9.0, gcc 3.2.2 > computer B: Turbo Linux 10,gcc 3.4.3 > computer C: Redhat 7.2, gcc 2.96 > computer D: Fedora core 6, gcc 3.4.6(the default version is 4.1.1, so I > reinstalled an old version on it) > All the gmx are compiled in float and mpi mode. > The results of mdrun (the final .gro file, the trajectory file and the energy > file) that start from the same .tpr file obtained on these computers are > totally different, but if I ran mdrun on one computer from this .tpr file > twice or more times, the results are all the same. So I don't know why the > "mdrun" compiled by different versions of gcc would give such different > results and which result should I trust. Does anybody know why it happens? I > beg for your help... > > this is the content of my .mdp file, I have modified nstlist, ns_type, pbc, > rlist, rvdw and rcoulomb for many times, but it does not work. > It is because MD is chaotic, and small differences in compilation, e.g. due to optimization will change the trajectory. However, your averages should be the same. Check potential energy after equilibration, and its fluctuations as well.
> title = > cpp = /usr/bin/cpp > include = > define = -DFLEXIBLE > > integrator = md > tinit = 0 > dt = 0.002 > nsteps = 12000 > init_step = 0 > comm-mode = Angular > nstcomm = 1 > comm-grps = > > bd-fric = 0 > ld-seed = 1993 > > emtol = 100 > emstep = 0.01 > niter = 20 > fcstep = 0 > nstcgsteep = 1000 > nbfgscorr = 10 > > nstxout = 100 > nstvout = 1000 > nstfout = 0 > nstcheckpoint = 1000 > nstlog = 1000 > nstenergy = 100 > nstxtcout = 0 > xtc-precision = 1000 > xtc-grps = > energygrps = > > nstlist = 1 > ns_type = grid > pbc = xyz > rlist = 0.9 > domain-decomposition = no > > coulombtype = Cut-off > rcoulomb-switch = 0 > rcoulomb = 1.2 > epsilon_r = 1 > epsilon_rf = 1 > vdw-type = Cut-off > rvdw-switch = 0 > rvdw = 0.9 > DispCorr = No > table-extension = 1 > energygrp_table = > fourierspacing = 0.12 > fourier_nx = 0 > fourier_ny = 0 > fourier_nz = 0 > pme_order = 4 > ewald_rtol = 1e-05 > ewald_geometry = 3d > epsilon_surface = 0 > optimize_fft = no > > gb_algorithm = Still > nstgbradii = 1 > rgbradii = 2 > gb_saltconc = 0 > > implicit_solvent = No > > Tcoupl = nose-hoover > tc-grps = System > tau-t = 0.1 > ref-t = 600 > Pcoupl = no > Pcoupltype = Isotropic > tau-p = 1 > compressibility = > ref-p = > andersen_seed = 815131 > > QMMM = no > QMMM-grps = > QMmethod = > QMMMscheme = normal > QMbasis = > QMcharge = > QMmult = > SH = > CASorbitals = > CASelectrons = > SAon = > SAoff = > SAsteps = > MMChargeScaleFactor = 1 > bOPT = > bTS = > > annealing = no > annealing_npoints = 11 > annealing_time = > annealing_temp = > > gen_vel = no > gen-temp = 600 > gen-seed = 173529 > > constraints = none > constraint-algorithm = Lincs > unconstrained-start = no > Shake-SOR = no > shake-tol = 0.0001 > lincs-order = 4 > lincs-iter = 1 > lincs-warnangle = 30 > morse = no > > energygrp_excl = > > disre = No > disre-weighting = Conservative > disre-mixed = no > disre-fc = 1000 > disre-tau = 0 > nstdisreout = 100 > orire = no > orire-fc = 0 > orire-tau = 0 > orire-fitgrp = > nstorireout = 100 > dihre = No > dihre-fc = 1000 > dihre-tau = 0 > nstdihreout = 100 > > free-energy = no > init-lambda = 0 > delta-lambda = 0 > sc-alpha = 0 > sc-power = 0 > sc-sigma = 0.3 > > ; Non-equilibrium MD stuff > acc-grps = > accelerate = > freezegrps = > freezedim = > cos-acceleration = 0 > deform = > > ; Electric fields > ; Format is number of terms (int) and for all terms an amplitude (real) > ; and a phase angle (real) > E-x = > E-xt = > E-y = > E-yt = > E-z = > E-zt = > > ; User defined thingies > user1-grps = > user2-grps = > userint1 = 0 > userint2 = 0 > userint3 = 0 > userint4 = 0 > userreal1 = 0 > userreal2 = 0 > userreal3 = 0 > userreal4 = 0 > > > YuXiang > [EMAIL PROTECTED] > 2007-11-05 > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- David van der Spoel, Ph.D. Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
