<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi,<DIV><BR class="khtml-block-placeholder"></DIV><DIV><DIV><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">With a plain cut-off one of the biggest sources of error is the</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">charge group based neighborlist.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">When I change the water topology from one charge group to</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">three (one for each atom) or when I used a shift function for the LJ</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I get 0 drift in double precision (300 ps) and about -85 kJ/mol/ns</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">for single precision.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">One can not expect that single precision does as good as double</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">precision. But the -85 kJ/mol/ns is already very good and comparable</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">to other errors introduced by the simulation setup, such a charge group</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">based neighborlists and PME approximations.</DIV></BLOCKQUOTE></DIV><DIV><FONT class="Apple-style-span" color="#0000DD"><BR class="khtml-block-placeholder"></FONT></DIV>The main problem in single precision are the constraints - in testing we've actually achieved perfect conservation even with constraints, as long as the integration/constraint part is perfomed in double (requires hacking). </DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>You can also play with ewald_rtol to improve energy conservation with PME. The current PME interacition form is optimized to be as close as possible to the "true" infinite coulomb sum - you could envision adding a small switching term to improve the energy conservation and/or zeroing the net force sum from the lattice part, but this again requires hacking.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Cheers,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Erik<BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><DIV>-----------------------------------------------------------</DIV><DIV>Erik Lindahl <<A href="mailto:lindahl@sbc.su.se">lindahl@sbc.su.se</A>></DIV><DIV>Assistant Professor, Stockholm Bioinformatics Center</DIV><DIV>Stockholm University, SE 106 91 Stockholm</DIV><DIV>Phone: +46 8 5537 8564 Fax: +46 8 5537 8214</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR class="Apple-interchange-newline"></SPAN> </DIV><BR></DIV></BODY></HTML>