On 9/4/13 10:18 AM, Steven Neumann wrote:
Thank you. i am using my own vdw tables so need a cut off.
Then I guess you have your answer. Finite cutoffs in vacuo can lead to serious
artifacts if you're not careful. Tread lightly.
-Justin
On Wed, Sep 4, 2013 at 3:13 PM, Justin Lemkul <jalem...@vt.edu> wrote:
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
-Justin
On Wed, Sep 4, 2013 at 3:09 PM, Justin Lemkul <jalem...@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
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
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Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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Department of Pharmaceutical Sciences
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Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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jalem...@outerbanks.umaryland.edu | (410) 706-7441
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