[gmx-users] how small rcoulomb can be
gauravgoeluta at gmail.com
Fri Jun 18 18:40:40 CEST 2010
I will re-ask my question as it didn't come out right in previous
mail. Read below.
On Wed, Jun 16, 2010 at 6:11 PM, Mark Abraham <mark.abraham at anu.edu.au> wrote:
> ----- Original Message -----
> From: Gaurav Goel <gauravgoeluta at gmail.com>
> Date: Thursday, June 17, 2010 5:21
> Subject: [gmx-users] how small rcoulomb can be
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> For my NPT/NVT simulations I'm using a BKS potential for dispersion
>> interactions (VdWtype=USER) which has a cut-off of 0.55
>> nm. I also
>> set rcoulomb=rlist=0.55 nm.
>> My first question is regarding the choice of rcoulomb=0.55nm. Any
>> thoughts on whether this rcoulomb is large enough to ascertain that
>> real space electrostatics interactions are fairly small (in comparison
>> to total coulombic interactions)?
> That's around half the size of typical rcoulomb values used for PME, so
> you'll need to adjust ewald_rtol and fourier_spacing to a considerable
> degree in order that the electrostatics your PME model is comparably
> accurate. If this model has been used with PME in the past, then you will
> have some guidance in its literature (though GROMACS does not make it easy
> to choose beta directly). This will mean the reciprocal-space processors are
> doing lots more work than normal, and you'll want to set -npme to be half of
> -np, or maybe zero. Even so, your parallel scaling will be noticeably worse
> than normal PME.
Thanks for your reply Mark. Any thoughts on instead increasing
rcoulomb and rlist. Will that be more efficient and/or accurate rather
than trying to adjust ewald_rtol and fourier_spacing with a very short
rcoulomb? In literature I found that the optimal value people have
used for beta is, beta*L=10.
In my simulations, for rcoulomb=0.55, beta*L=15.52
rcoulomb=0.9, beta*L= 9.49
How can I obtain the magnitude of maximum wave vector (i.e., 'm' in
Eq. 4.159 of manual 4.0)?
I have a separate question in regards to (conserved) energy drift in a
I first equilibrated my system for 1 ns in NPT ensemble. Then, I
turned-off the pressure coupling, further equilibrated my system for 1
ns In NVT ensemble [N=2160, V=20.43 nm^3, T=4000K; rcoulomb=rlist=0.9,
rvdw=0.55, nstlist=5]. Then in a production run of 3.5ns I get
following energy drifts:
Statistics over 3549897 steps [ 1000.0000 thru 4549.8960 ps ], 1 data sets
All averages are exact over 3549897 steps
Energy Average RMSD Fluct. Drift Tot-Drift
Conserved En. -3.65264e+06 18936 73.1027 18.4782
i.e. drift=0.16 kT/ns.
If nstlist=10, drift= 0.5kT/ns
Should I worry about these drifts?
>> My second question is in regards to doing long (~15-100 ns) NVE
>> simulations. It appears using coulombtype=PME-Switch will be the best
>> option to accurately conserve energy. Any thoughts on how to choose
>> rcoulomb_switch and rcoulomb?
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