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Hi,<br><br>You don't say at all what your systems looks like, so it is difficult to give<br>proper advice.<br>As far as electrostatics is concerned, this scaling has very little effect<br>on the accuracy of the results.<br>For the Lennard-Jones interaction however, the longer cut-off<br>puts many more pairs in the interaction list. If you were using<br>dispersion correction, this longer LJ cut-off will make the results<br>more accurate. If you were not using dispersion correction, you<br>will get a lower pressure or higher density (depending on if you<br>are simulating NVT or NPT).<br><br>A low density will usually cause this large shift in optimal settings.<br><br>Berk<br><br>> Date: Thu, 10 Sep 2009 15:35:49 +0100<br>> From: Jennifer.Williams@ed.ac.uk<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] large scaling required to acheive optimal mesh load<br>> <br>> Hello user,<br>> <br>> I am simulating a unit cell with dimensions 70x70x38 nm using PME. I <br>> started out with a cut-off of rvdw = rcoloumb = rlist=0.9 and a <br>> Spacing for the PME/PPPM FFT grid= 0.12, optimize fft = yes<br>> <br>> I get the following output when I compile the .tpr file:<br>> <br>> Using a fourier grid of 60x60x33, spacing 0.117 0.117 0.117<br>> Estimate for the relative computational load of the PME mesh part: 0.97<br>> <br>> NOTE 1 [file SMO_CO2.top, line 2159]:<br>> The optimal PME mesh load for parallel simulations is below 0.5<br>> and for highly parallel simulations between 0.25 and 0.33,<br>> for higher performance, increase the cut-off and the PME grid spacing<br>> <br>> I did a number of test-runs increasing the cut-offs and the grid <br>> spacing by a factor of themselves. However I had to nearly double the <br>> cut-off and grid spacing in order to get the PME mesh load below 50. <br>> From the forum notes on the topic I got the impression that only a <br>> small scaling factor was needed.<br>> <br>> My question is, are the values which I have achieved reasonable?<br>> <br>> Cut-off: 1.665 and grid spacing 0.222<br>> <br>> This is the output using these values....<br>> <br>> Checking consistency between energy and charge groups...<br>> Calculating fourier grid dimensions for X Y Z<br>> Using a fourier grid of 32x32x18, spacing 0.219 0.219 0.215<br>> Estimate for the relative computational load of the PME mesh part: 0.38<br>> This run will generate roughly 63 Mb of data<br>> writing run input file...<br>> <br>> Does changing these values have any effect on the results of the mdrun <br>> or only on the speed?<br>> <br>> Thanks in advance,<br>> <br>> Jenny<br>> <br>> <br>> <br>> -- <br>> The University of Edinburgh is a charitable body, registered in<br>> Scotland, with registration number SC005336.<br>> <br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />See all the ways you can stay connected <a href='http://www.microsoft.com/windows/windowslive/default.aspx' target='_new'>to friends and family</a></body>
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