이 선주 wrote: > Hello All, > > I have been doing membranes simulations using the computer nodes in > UTEXAS supercomputing center. Each board contains two Xeon Intel > Duo-Core 64-bit processors (4 cores in all) and nodes are interconnected > with InfiniBand technology. > The performance is great. However, I have got weird results if I > increase the number of processors more than 12. Even though the bilayer > is still intact, one or two lipids were popped out of the membrane not > long after the simulation was started. > To make sure that it is not the problem due to different initial > conditions, I ran two separate md simulations starting from the same > structure and velocities on each atom but only with different number of > processors, 8 and 16. > As expected, the job with 8 processors resulted in the intact membrane > but a lipid was pulled out of the membrane in the job run with 16 > processors. > > So far, I could not find out the cause of this problem. Does anyone have > any thought about this problem? > Thank you > Sunjoo > Please check bugzilla to see if your problem is listed there. It looks a bit like:
http://bugzilla.gromacs.org/show_bug.cgi?id=109 -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users 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
