<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><DIV>Box correction is already done automatically in Gromacs (ns.c) - what I meant here was "fairly skewed compared to a rectangular box", e.g. 30 degrees. Since the charge spreading has to be done on a triclinic grid in that case it is no longer radially uniform, which _could_ affect accuracy a bit (i.e., you might need to user higher interpolation order).</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Cheers,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Erik</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>On Mar 30, 2006, at 2:05 PM, Tsjerk Wassenaar wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><BR>Hi Erik,<BR><BR>Actually a severely skewed box is basically an imaginary concept. For normal MD dimensions it is always possible to perform a simple transformation to transform a box into one which complies to the Gromacs rules in an optimal way. That is, if the box vector lengths are around the same order of magnitude. Maybe a routine for this could be added to gromacs (editconf/genbox/grompp) to fix skewed boxes, and to optimize the use of PME. I added a routine to my version of pbc.c which could provide a basis. This does not change the system, but only uses other, equally valid, lattice vectors. Let me know if you're interested.<BR><BR>Tsjerk<BR><BR><DIV><SPAN class="gmail_quote">On 3/30/06, <B class="gmail_sendername"> Erik Lindahl</B> <<A href="mailto:lindahl@sbc.su.se">lindahl@sbc.su.se</A>> wrote:</SPAN><BLOCKQUOTE class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <DIV style="direction: ltr;">Hi,<DIV><BR></DIV><DIV>As Tsjerk wrote we always work with the triclinic representation in the code, which fills up space nicely. Due to rounding it might not be a _perfect_ representation of e.g. a hexagonal box, truncated octahedron, rhombic dodecahedron, etc., but that shouldn't affect the physics of the triclinic box.</DIV><DIV><BR></DIV><DIV>The reason I first asked about boxes is that the PME grid too has to be triclinic for such boxes, and I don't think anybody has done any detail PME accuracy analysis in the case of severely skewed boxes. </DIV><DIV><BR></DIV><DIV>Cheers,</DIV></DIV><DIV style="direction: ltr;"><SPAN class="sg"><DIV><BR></DIV><DIV>Erik</DIV><DIV><BR></DIV></SPAN></DIV><DIV style="direction: ltr;"><DIV><DIV></DIV><DIV style="direction: ltr;"> <SPAN class="e" id="q_10a4aee57e3a647c_3"><DIV>On Mar 30, 2006, at 9:43 AM, Tsjerk Wassenaar wrote:</DIV><BR></SPAN></DIV><DIV style="direction: ltr;"><BLOCKQUOTE type="cite"></BLOCKQUOTE></DIV><DIV style="direction: ltr;"> <SPAN class="e" id="q_10a4aee57e3a647c_5">Hi Michael,<BR><BR>It will in any case still fill up space in a periodic way. That can be done with an infinite number of triclinic boxes, of which the formal (perfectly regular) truncated octahedron is only one. Besides, the shift vectors are used to calculate the distances between particles, determine the neighbour lists, etc. If the coordinates are only stored with a certain precision, there is no point in having lattice vectors (box vectors) available with higher precision. You may want to read a bit on periodic boundary conditions from Henk Bekker (notably his 1996 JCC paper). <BR><BR>By the way.., don't use the truncated octahedron (unless it's for comparison), try a rhombic dodecahedron instead. It's smaller and most likely better in terms of the simulation results.<BR><BR>Cheers,<BR><BR>Tsjerk <BR><BR><DIV><SPAN class="gmail_quote">On 3/30/06, <B class="gmail_sendername">Michael Shirts</B> <<A href="mailto:mrshirts@gmail.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">mrshirts@gmail.com </A>> wrote:</SPAN><BLOCKQUOTE class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> That would be pbc (periodic boundary conditions), not pdc (who knows<BR> what that is), of course . . .<BR><BR>On 3/30/06, Michael Shirts <<A href="mailto:mrshirts@gmail.com" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">mrshirts@gmail.com</A>> wrote:<BR>> So, to get a truncated octahedron, or some other shape, you use <BR>> certain ratios for the box vectors as detailed in the manual. But the<BR>> box vectors in the .gro file are truncated to a certain precision, so<BR>> don't exactly meet these ratios. What is the consequence of not <BR>> exactly meeting these ratios? It won't precisely fill space in a<BR>> periodic way -- so does it mess up the pbc in some way? Anyone know?<BR>> Any experiences? Should I make sure the ratios are correct up to <BR>> machine precision? Is there a way to handle this more robustly?<BR>><BR>> Thanks,<BR>> Michael Shirts<BR>> Research Fellow<BR>> Columbia University<BR>><BR>_______________________________________________ <BR>gmx-users mailing list <A href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users@gromacs.org</A><BR><A href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)"> http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to <A href="mailto:gmx-users-request@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)"> gmx-users-request@gromacs.org</A>.<BR>Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://www.gromacs.org/mailing_lists/users.php </A><BR></BLOCKQUOTE></DIV><BR><BR clear="all"><BR>-- <BR><BR>Tsjerk A. Wassenaar, M.Sc.<BR>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<BR>Dept. of Biophysical Chemistry<BR>University of Groningen<BR> Nijenborgh 4<BR>9747AG Groningen, The Netherlands<BR>+31 50 363 4336<BR></SPAN></DIV><DIV style="direction: ltr;"><DIV style="margin: 0px;">_______________________________________________</DIV></DIV><DIV style="direction: ltr;"> <SPAN class="q"><DIV style="margin: 0px;">gmx-users mailing list<SPAN> </SPAN><A href="mailto:gmx-users@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">gmx-users@gromacs.org</A></DIV> <DIV style="margin: 0px;"><A href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin: 0px;"> Please don't post (un)subscribe requests to the list. Use the<SPAN> </SPAN></DIV><DIV style="margin: 0px;">www interface or send it to <A href="mailto:gmx-users-request@gromacs.org" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)"> gmx-users-request@gromacs.org</A>.</DIV><DIV style="margin: 0px;">Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://www.gromacs.org/mailing_lists/users.php </A></DIV> </SPAN></DIV><DIV style="direction: ltr;"></DIV><BR></DIV> </DIV><BR>_______________________________________________<BR>gmx-users mailing list <A onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A><BR><A onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank"> http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please don't post (un)subscribe requests to the list. Use the<BR>www interface or send it to <A onclick="return top.js.OpenExtLink(window,event,this)" href="mailto:gmx-users-request@gromacs.org"> gmx-users-request@gromacs.org</A>.<BR>Can't post? Read <A onclick="return top.js.OpenExtLink(window,event,this)" href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php </A><BR><BR></BLOCKQUOTE></DIV><BR><BR clear="all"><BR>-- <BR><BR>Tsjerk A. Wassenaar, M.Sc.<BR>Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<BR>Dept. of Biophysical Chemistry<BR>University of Groningen <BR>Nijenborgh 4<BR>9747AG Groningen, The Netherlands<BR>+31 50 363 4336<BR><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-users mailing list<SPAN class="Apple-converted-space"> </SPAN><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. 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