Hello Gromacs users,<br><br>I've been doing some simple NVT simulations of Lennard-Jones particles using the built-in 12-6 potential and a tabulated version (vdwtype=user) of this same potential. Both give practically identical results for the density and pressure, but differ in the chemical potential computed using the "tpi" mode in mdrun. The chemical potentials end up having the same order of magnitude, but the chemical potential for the built-in function seems to be systematically lower, e.g. 3.48 kJ/mol (built-in) vs. 6.26 kJ/mol (tabulated). The difference is smaller for the double precision version of mdrun (e.g. 7.19 kJ/mol vs. 7.55 kJ/mol). <br>
<br>I ran some simulations in debug mode, and looked at the energies and coordinates of each insertion. It seems like 99.9% percent of the them are identical, but when the insertion energy is especially high, the simulation using the built-in function just outputs some random number, whereas the one with the table computes something around 5e18, the number to which the table plateaus as r goes to 0.<br>
<br>Here is an example using mdrun_d (I've removed extraneous lines from the logging file):<br><br>Built-in function:<br><br> Insertion # Energy x y z<br>TPI 6205 2.23227e+06 0.00961 0.91659 1.56009<br>
TPI 6206 2.29990e+06 0.01536 0.84120 1.57042<br>TPI 6207 6.44107e+07 -0.01544 0.89706 1.55119<br>TPI 6208 2.57252e+07 -0.00345 0.85349 1.55140<br>TPI 6209 1.65644e+07 -0.02364 0.87913 1.57432<br>
TPI 6210 6.26137e+03 0.83206 0.68462 0.46606<br>TPI 6211 9.31542e+09 0.78445 0.71232 0.44283<br>TPI 6212 9.63046e+11 0.80033 0.67289 0.44387<br>TPI 6213 7.00802e+10 0.78840 0.69046 0.44094<br>
<br>Tabulated function:<br><br> Insertion # Energy x y z<br>TPI 6205 2.23227e+06 0.00961 0.91659 1.56009<br>TPI 6206 2.29990e+06 0.01536 0.84120 1.57042<br>
TPI 6207 6.44107e+07 -0.01544 0.89706 1.55119<br>TPI 6208 2.57252e+07 -0.00345 0.85349 1.55140<br>TPI 6209 1.65644e+07 -0.02364 0.87913 1.57432<br>TPI 6210 6.01461e+18 0.83206 0.68462 0.46606<br>
TPI 6211 9.31542e+09 0.78445 0.71232 0.44283<br>TPI 6212 9.63046e+11 0.80033 0.67289 0.44387<br>TPI 6213 7.00802e+10 0.78840 0.69046 0.44094<br><br>Notice that for insertion #6210, the built-in function outputs 6.26137e+03. I checked the coordinates of the other particles in this frame, and there is a particle at (0.829, 0.686, 0.466), so I would think the insertion energy would be really high; hence the value of 6e18 for the tabulated function.<br>
<br>I am using Gromacs 4.0.7 straight from the Ubuntu lucid repository (<a href="http://packages.ubuntu.com/lucid/gromacs" target="_blank">http://packages.ubuntu.com/lucid/gromacs</a>). I am running it on the i386 architecture.<br>
<br>Thanks,<br><br>Kevin<br>
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