[gmx-users] The optimal PME mesh load for parallel simulations is below 0.5
jalemkul at vt.edu
Wed Sep 4 16:13:07 CEST 2013
On 9/4/13 10:11 AM, Steven Neumann wrote:
> Thank you! Would you suggest just a cut-off for coulmb?
Not a finite one. The best in vacuo settings are:
pbc = no
rlist = 0
rvdw = 0
rcoulomb = 0
nstlist = 0
vdwtype = cutoff
coulombtype = cutoff
> On Wed, Sep 4, 2013 at 3:09 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> 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
>>> 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
>> 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
>> jalemkul at outerbanks.umaryland.**edu <jalemkul at outerbanks.umaryland.edu> | (410)
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Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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