Hello Justin, Thanks.
1- I changed the setting below because of the note I used to get: NOTE 1 [file aminoacids.dat, line 1]: The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing Also, earlier on I read one of your messages about the trade off between accuracy and speed for this setting and that no systematic study has been done how exactly accuracy is changing. I actually need to work with systems with 40 000 atoms or even more and electrostatics slows down my runs to a great extent. Can you please give an idea on to what extent the accuracy affects the result say for fourierspacing = 0.2 . I mean it affects second decimal or...? I need to go for a setting which speeds up calculations as much as possible while being reasonable. How would you deal with this? What value would you pick? Thank you, moeed > fourierspacing = 0.3 >> > > You're setting yourself up for inaccurate PME calculations with this. Use > 0.1 - 0.12 unless you've got some compelling reason to decrease your > accuracy. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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 > 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 > -- Moeed Shahamat Graduate Student (Materials Modeling Research Group) McGill University- Department of Chemical Engineering Montreal, Quebec H3A 2B2, Canada Web: http://mmrg.chemeng.mcgill.ca/pages/current-group-members/moeed-shahamat.php Web:http://mmrg.chemeng.mcgill.ca/
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