Dear Sir, That is true as the number of the frames increased the memory had almost reached 95% but still it has been in 95% since long and CPU usage drops down to 1.5 -2 % but in many cases i have seen that still it will run (off course slowly) and finish. But this was too long. So any suggestions?
Thank you Kavya On Thu, Jul 12, 2012 at 3:39 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > On 7/12/12 4:51 AM, Kavyashree M wrote: >> >> Dear Gromacs users, >> >> I was running the saltbridge calculations for a dimeric >> protein simulation using g_saltbr, But its taking very >> long time, almost four days still its not completed. >> Could anyone has suggestion regarding this issue? I am >> using the same system - >> Intel(R) Core(TM) i7-2600 CPU @ 3.40GHz >> where i ran MD. Please give some suggestion as to how to >> increase the speed of calculation. >> Command i issued was: >> g_saltbr -f ../traj.xtc -s md.tpr -t 0.4 -sep >> > > g_saltbr calculates properties of all possible ionic pairs in the system, so > if there are many, the calculation might take a long time. Four days sounds > ridiculous, and perhaps the program has frozen by exhausting the available > memory. > > -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 > > ======================================== > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * 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 gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
