I did not follow your previous discussion, but I am sure you need to quantitatively estimate the slowness of your simulation.
For instance, you can compute the factor by dividing the execution time using GBSA by the execution time for protein in vacuum. The people often complain it is slow, whereas it is exactly as it should be. Dr. Vitaly V. Chaban MEMPHYS - Center for Biomembrane Physics Department of Physics, Chemistry and Pharmacy University of Southern Denmark Campusvej 55, 5230 Odense M, Denmark On Fri, Nov 2, 2012 at 5:23 PM, Albert <mailmd2...@gmail.com> wrote: > Hello Vitaly: > > thanks a lot for kind comments. > Do you have any idea why the running is so slow? Especially considering it > is with GBSA model and my protein is only with 240 aa. > > thank you very much > best > Albert > > On 11/02/2012 04:30 PM, Dr. Vitaly Chaban wrote: >>>> >>>> If I turn this option on, such as: >>>> >>>> pcouple=Isotropic >>>> >>>> it is said: >>>> >>>> >>>> ERROR 1 [file eq.mdp, line 78]: >>>> Pressure coupling not enough values (I need 1) >>>> >>>> >>>> WARNING 1 [file eq.mdp]: >>>> Turning off pressure coupling for vacuum system >> >> >> You canNOT use pressure coupling without PBC in gromacs. >> >> >> Dr. Vitaly V. Chaban >> MEMPHYS - Center for Biomembrane Physics >> Department of Physics, Chemistry and Pharmacy >> University of Southern Denmark >> Campusvej 55, 5230 Odense M, Denmark >> >> >> -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
