Hi Brent,
Try turning off the long range VDW correction and see if the problems still exists. vdwmeth=0 in ewald namelist.
All the best
Ross
> On Oct 2, 2015, at 10:54 AM, Brent Krueger <kruegerb.hope.edu> wrote:
>
> Dear AMBER experts,
>
> A student of mine is having an interesting problem come up that I do not
> understand. We are modeling salt crystals and have done extensive
> convergence testing for all of the simulations we are running. We have
> sorted out everything except one issue. We are building salt crystals and
> evaluating their energies (no dynamics) using periodic boundary
> conditions. We have run calculations using systems of various sizes. In
> our case the smallest unit is 8 ions: 4 Na+ and 4 Cl- forming a small
> cube. We have built systems that are 5x5x5, 10x10x10, and so on of these
> tiny units. It should be the case that the system energy on a per ion
> basis is exactly the same for all of these different systems. However,
> this is not quite the case and it turns out that the VDW energy is the
> source of the inconsistency. The VDW energy is the same out to 8 or 9
> digits for systems with 5, 10, 15, and 20 units (per edge), but then there
> is a significant jump (0.3%) in energy between 20 and 25 units. I've
> inserted a table and a plot below that illustrate this. Note that the
> table has total energy, electrostatic, and vdw parsed out. The figure has
> just the total energy. And note that in the table we divided by (2N)^3 so
> it really is the energy per particle, whereas we just divided by N^3 in the
> figure; don't be distracted by the factor of 8.
>
> We have double-checked that the mdin files are identical, so I don't think
> it is the case that we have made a silly mistake. Does this dependence of
> the system VDW energy on the system size ring any bells for anyone? For
> now we are assuming that the 5--20 data are 'correct' and that there is
> something wrong with the others, but if anyone has any insight to this, I
> would love to hear it.
>
> Thanks,
> Brent
>
>
> N Atom pairs per crystal edge Energy (kcal/mol) Energy/(2N)3 Eelec Eelec/
> (2N)3 Evdw Evdw/(2N)3 5 -95652.9106 -95.6529106 -102703.1589 -102.7031589
> 7050.2482 7.0502482 10 -765223.2851 -95.65291064 -821625.2708 -102.7031589
> 56401.9857 7.050248213 15 -2582628.587 -95.65291064 -2772985.289
> -102.7031589 190356.7016 7.050248207 20 -6121786.281 -95.65291064
> -6573002.167 -102.7031589 451215.8854 7.050248209 25 -11953946.43
> -95.63157141 -12837894.86 -102.7031589 883948.4309 7.071587447 30
> -20656397.79 -95.63147123 -22183882.31 -102.7031588 1527484.525 7.071687614
> 35 -32802143.74 -95.63307213 -35227183.48 -102.7031588 2425039.741
> 7.070086709 40 -48964521.92 -95.63383187 -52584017.33 -102.7031589
> 3619495.414 7.06932698 45 -69716793.27 -95.63346127 -74870602.81
> -102.7031589 5153809.542 7.069697588
>
>
>
> [image: Inline image 2]
>
>
> --
> _______________________________________________
> Brent P. Krueger.....................phone: 616 395 7629
> Professor.................................fax: 616 395 7118
> Hope College..........................Schaap Hall 2120
> Department of Chemistry
> Holland, MI 49423
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Received on Fri Oct 02 2015 - 11:30:03 PDT
