Hi Dechang, it is normal that results are not binary identical if you compare the "same" MD system on different numbers of processors. If you use PME then you will probably get slightly different charge grids for 2 and for 16 processors - since the charge grid has to be divisible by the number of CPUs in x- and y-direction. Even if you manually set the grid dimensions to be the same for both cases, your simulations could diverge when using version 3.x of the FFTW. This version has a build-in timer and chooses the fastest of several algorithms which could be another even in two runs on the same number of processors - depending on the timing results. With different algorithms you get slight differences in the last digit of the computed numbers (rounding / truncation / order of evaluation) which will then grow during the simulation and lead to diverging trajectories. Of course the averaged properties of the simulation are unaffected by those differences and should be the same if averaged long enough. You could use FFTW 2.x and manually set the FFT grid size to the same value for the 2 and 16 CPU case - but I am not shure if this is enough to get binary identical results. You could also repeat your simulations several times with (slightly) different starting conditions (maybe different starting velocities) to get a better picture of the average behaviour of your system. If in all 16 processor cases you see the proteins diverge and in all 2 processor cases you see them converge, I would guess something is wrong.
Hope that helps, Carsten Dechang Li wrote: > Dear all, > > I used Gromacs3.3.1 to do a simulation about two proteins in water(tip3p). > I run two similar simulations, one for 2 cpus, while the other for 16 cpus. > The two simulations have the same .gro, .top, and the same .mdp files. I found > the results were not the same. In the 2 cpus simulation, the two proteins > run closer and closer. But they run apart in the 16 cpus simulation. > Is that normal the different results when using different number cpus? The > size of my simulation box is 9*7*7. > > > > > > > > Best regards, > > 2007-12-5 > > > ========================================= > Dechang Li, PhD Candidate > Department of Engineering Mechanics > Tsinghua University > Beijing 100084 > PR China > > Tel: +86-10-62773779(O) > Email: [EMAIL PROTECTED] > ========================================= > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > 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 -- Dr. Carsten Kutzner Max Planck Institute for Biophysical Chemistry Theoretical and Computational Biophysics Department Am Fassberg 11 37077 Goettingen, Germany Tel. +49-551-2012313, Fax: +49-551-2012302 http://www.mpibpc.mpg.de/research/dep/grubmueller/ http://www.gwdg.de/~ckutzne _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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