On 9/4/13 10:03 AM, Steven Neumann wrote:
DEa Users,
My system involves protein in vacuum - 80 atoms in box of 9x9x9 nm3. I want
to use PME in my mdp:
rcoulomb = 2.0
coulombtype = PME
pme_order = 4
fourierspacing = 0.12
The cutoff needs to stay like this, I have my own tables with VDW, bonds,
angles and dihedrals.
i got the NOTE:
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
what setting would you suggest to use on 8 CPUs?
I would suggest not using PME :) The problem is PME is extremely inefficient in
vacuo because it spends a lot of time doing nothing due to the empty space.
Moreover, you're not likely really simulating in vacuo at that point because
you've got PBC and therefore are really doing a simulation in more of a diffuse
crystal environment, so there are probably artifacts.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
--
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
