<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Hi Malin,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>From my previous (pretty limited) experience with polymers I know that it is pretty common to run them without constraints, using 1 fs timesteps, and bond force constants that are significantly weaker than normal. </DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>You can check the force field parameters used in the d.polych2 benchmark from the Gromacs website.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Cheers,</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Erik</DIV><DIV><BR><DIV><DIV>On Nov 17, 2005, at 10:41 AM, Malin Bergenstråhle wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"> <DIV><FONT face="Arial" size="2">Hi,</FONT></DIV> <DIV><FONT face="Arial" size="2"></FONT> </DIV> <DIV><FONT face="Arial" size="2">I am simulating a system of infinite polymer chains using pbc=full and LINCS bond constraints. </FONT></DIV> <DIV><FONT face="Arial" size="2">My system is unreliable and sometimes the simulations crash due to LINCS complaining about too large bond rotations. </FONT></DIV> <DIV><FONT face="Arial" size="2">I have now noted that it seems like LINCS gives warnings of the kind:</FONT></DIV> <DIV><FONT face="Arial" size="2"></FONT> </DIV> <DIV><FONT face="Arial" size="2">Step 22525, time 67.575 (ps) LINCS WARNING<BR>relative constraint deviation after LINCS:<BR>max 0.000029 (between atoms 22 and 23) rms 0.000004<BR>bonds that rotated more than 30 degrees:<BR> atom 1 atom 2 angle previous, current, constraint length<BR> 347 348 30.6 0.1000 0.1000 0.1000</FONT></DIV> <DIV><FONT face="Arial" size="2"></FONT> </DIV> <DIV><FONT face="Arial" size="2">and the atoms are always situated on different sides of a periodic bound. A question that now arises is whether this could be a bug with pbc=full or whether there is a problem with my system. I am using Gromacs 3.3.</FONT></DIV> <DIV><FONT face="Arial" size="2"></FONT> </DIV> <DIV><FONT face="Arial" size="2">Any suggestions about how I could check this or whatever about whatever the problem could be I would be grateful.</FONT></DIV> <DIV><FONT face="Arial" size="2"></FONT> </DIV> <DIV><FONT face="Arial" size="2">Best regards,</FONT></DIV> <DIV><FONT face="Arial" size="2"></FONT> </DIV> <DIV><FONT face="Arial" size="2">Malin</FONT></DIV><FONT face="Arial" size="2"> <DIV><BR></DIV></FONT><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</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><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. Use the<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.</DIV> </BLOCKQUOTE></DIV><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>