The average of all my variations contain about 802780 atoms.
Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering [email protected] On Jan 3, 2013, at 9:36 PM, Justin Lemkul <[email protected]> wrote: > > > On 1/3/13 9:33 PM, Xu Dong Huang wrote: >> Actually, I correct myself, it's not even a 85x85x85 system, it's a 45x45x45 >> box system with water solvent + large multiple solutes. >> > > Performance depends mostly on the number of atoms. You haven't provided that > information, so it's hard to judge what you might expect. > > -Justin > >> Xu Dong Huang >> Chemical & Biochemical Engineering >> Rutgers School of Engineering >> [email protected] >> >> On Jan 3, 2013, at 9:29 PM, Xu Dong Huang <[email protected]> wrote: >> >>> Dear gromac users, >>> >>> I submitted my NPT run into a MPI cluster. The size of my run system is an >>> 85x85x85 box filled with water solvent. and I set NPT steps to be 1000000 >>> (1million) with dt 0.02. The log says It will finish sometime in mid or >>> towards end of february. >>> >>> Is that normal for a NPT run of that size? Or am I just faced with slow >>> technology. Or am I doing something wrong (I requested 6 cores for my run) >>> Please let me know, thanks. >>> >>> Xu Dong Huang >>> Chemical & Biochemical Engineering >>> Rutgers School of Engineering >>> [email protected] >>> >>> -- >>> gmx-users mailing list [email protected] >>> 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 [email protected]. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 [email protected] > 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 [email protected]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
