<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><BR><DIV><DIV>19 apr 2007 kl. 03.45 skrev Venky Krishna:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite">Hi George,<DIV><BR class="khtml-block-placeholder"></DIV><DIV>I usually delete/move the molecules reported to have high force values in the minimization steps. A better thing would be to start with a box which has sufficient intermolecular distance again by deleting molecules which are very close to each other (use the g_mindist program) and then energy minimize the system. Btw...did you define FLEXIBLE for water molecules during your em runs?</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Best</DIV><DIV>Venky</DIV><DIV><BR><DIV><DIV>On Apr 18, 2007, at 5:24 PM, George Abadir wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"> Hi,<BR> I am doing an energy minimization for a carbon nanotube (end capped with hydrogen atoms) in a box of water. I get the following message:<BR> <FONT color="#3333ff">" Stepsize too small, or no change in energy.<BR> Converged to machine precision,<BR> but not to the requested precision Fmax < 10<BR> <BR> Double precision normally gives you higher accuracy.<BR> You might need to increase your constraint accuracy, or turn off constraints altogether (set constraints = none in mdp file)<BR> <BR> Steepest Descents converged to machine precision in 1836 steps, but did not reach the requested Fmax < 10.<BR> Potential Energy = -2.4277438+06<BR> Maximum force = 5.9858018+03 on atom 13<BR> Norm of force = 5.1364398+04"</FONT><BR> <BR> The potential energy is extremely low and the maximum force is considerably large. I turned off the constrained and tried other energy minimization methods but still got the same error (with different magnitudes of the force and energy of course). Is it likely that double precision simulation can make such a big difference? If not (which I think) is there any other way to solve the problem?<BR> <BR></BLOCKQUOTE></DIV></DIV></BLOCKQUOTE><BR>I wouldn't call this an error. The minimization converged, and your potential energy is low. There is no problem to solve.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>/Erik</DIV><DIV><BR><BLOCKQUOTE type="cite"><DIV><DIV><BLOCKQUOTE type="cite"> Thank you very much in advance,<BR> George Abadir<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 search the archive at <A href="http://www.gromacs.org/search">http://www.gromacs.org/search</A> before posting!</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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Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</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; "><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; "><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; "><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; "><BLOCKQUOTE type="cite"></BLOCKQUOTE><DIV>_______________________________________________</DIV><DIV>Erik Marklund, PhD student</DIV><DIV>Laboratory of Molecular Biophysics,</DIV><DIV>Dept. of Cell and Molecular Biology, Uppsala University.</DIV><DIV>Husargatan 3, Box 596,<SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>75124 Uppsala, Sweden</DIV><DIV>phone:<SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>+46 18 471 4537<SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>fax: +46 18 511 755</DIV><DIV><A href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</A><SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>http://xray.bmc.uu.se/molbiophys</DIV><BR class="Apple-interchange-newline"></SPAN></SPAN></SPAN></SPAN> </DIV><BR></BODY></HTML>