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 <[email protected]> wrote: > > > ----- Original Message ----- > From: Gaurav Goel <[email protected]> > Date: Thursday, June 17, 2010 5:21 > Subject: [gmx-users] how small rcoulomb can be > To: Discussion list for GROMACS users <[email protected]> > >> 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 NVT simulation. 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 65595.7 i.e. drift=0.16 kT/ns. If nstlist=10, drift= 0.5kT/ns Should I worry about these drifts? -Gaurav > > Mark > >> 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? >> >> Thanks, >> Gaurav >> -- >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search >> before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
