Dear Justin, Thanks a lot, your suggestions helped me a lot.
With Regards, Swati On Sun, Mar 3, 2013 at 1:22 AM, Justin Lemkul <[email protected]> wrote: > > > On 3/2/13 1:42 AM, swati rana wrote: > >> Hi Justin, >> >> Thanks a lot, that suggestion of yours helped. I am on the equilibration >> step and its running but nothing is happening on the terminal its just >> stagnant. Is it fine because its more than 17 hrs now. Is there some >> problem. >> After running the second command nothing is happening on the terminal. >> >> grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr >> >> mdrun -deffnm nvt >> >> I am sorry as it is not a reasonable question to ask but i am just asking >> out of curiosity and lack of time. >> >> > If you're trying to run an MD simulation in serial, you'll get terrible > performance unless the system is very small (a few hundred atoms). Most MD > is conducted in parallel on high-performance computing clusters, or at the > very least on a multi-core workstation, again using parallelization. > > You won't get constant output in either case, since I/O is buffered and > write intervals depend on what you specify in the .mdp file. In any case, > if you're getting poor performance, you're probably simply asking your > computer to do something it's incapable of handling efficiently. > > > -Justin > > -- > ==============================**========== > > 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
