<div>Hi Tsjerk,</div> <div>Many thanks for your suggestions.After <FONT size=3><FONT face="Times New Roman"><B><SPAN style="FONT-FAMILY: TimesNewRoman,Bold; mso-bidi-font-family: 'TimesNewRoman,Bold'">"grompp -f </SPAN></B><SPAN style="FONT-FAMILY: TimesNewRoman; mso-bidi-font-family: TimesNewRoman">em.mdp </SPAN><B><SPAN style="FONT-FAMILY: TimesNewRoman,Bold; mso-bidi-font-family: 'TimesNewRoman,Bold'">-c </SPAN></B><SPAN style="FONT-FAMILY: TimesNewRoman; mso-bidi-font-family: TimesNewRoman">trp_b4em.pdb </SPAN><B><SPAN style="FONT-FAMILY: TimesNewRoman,Bold; mso-bidi-font-family: 'TimesNewRoman,Bold'">-p </SPAN></B><SPAN style="FONT-FAMILY: TimesNewRoman; mso-bidi-font-family: TimesNewRoman">trp.top </SPAN><B><SPAN style="FONT-FAMILY: TimesNewRoman,Bold; mso-bidi-font-family: 'TimesNewRoman,Bold'">-o </SPAN></B><SPAN style="FONT-FAMILY: TimesNewRoman; mso-bidi-font-family: TimesNewRoman">trp_em.tpr " comand there was no warning message.Then I did mdrun (
<B><SPAN style="FONT-FAMILY: TimesNewRoman,Bold; mso-bidi-font-family: 'TimesNewRoman,Bold'">mdrun -s </SPAN></B><SPAN style="FONT-FAMILY: TimesNewRoman; mso-bidi-font-family: TimesNewRoman">trp_em.tpr </SPAN><B><SPAN style="FONT-FAMILY: TimesNewRoman,Bold; mso-bidi-font-family: 'TimesNewRoman,Bold'">-o </SPAN></B><SPAN style="FONT-FAMILY: TimesNewRoman; mso-bidi-font-family: TimesNewRoman">trp_em.trr </SPAN><B><SPAN style="FONT-FAMILY: TimesNewRoman,Bold; mso-bidi-font-family: 'TimesNewRoman,Bold'">-c </SPAN></B><SPAN style="FONT-FAMILY: TimesNewRoman; mso-bidi-font-family: TimesNewRoman">trp_b4pr.pdb </SPAN><B><SPAN style="FONT-FAMILY: TimesNewRoman,Bold; mso-bidi-font-family: 'TimesNewRoman,Bold'">-g </SPAN></B><SPAN style="FONT-FAMILY: TimesNewRoman; mso-bidi-font-family: TimesNewRoman">em.log </SPAN><B><SPAN style="FONT-FAMILY: TimesNewRoman,Bold; mso-bidi-font-family: 'TimesNewRoman,Bold'">-e </SPAN></B><SPAN style="FONT-FAMILY: TimesNewRoman; mso-bidi-font-family:
TimesNewRoman">em.edr ) and it was finished but</SPAN><B><SPAN style="FONT-FAMILY: TimesNewRoman,Bold; mso-bidi-font-family: 'TimesNewRoman,Bold'"><?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></B></div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none">it gave warning message(Warning: 1-4 interaction between 2100 and 2105 at distance 15.231 which is larger than the 1-4 table size 1.000 nm.These are ignored for the rest of the simulation.This usually means your system is exploding if not, you should increase table-extension in your mdp file)<BR>And after second <STRONG>grommp </STRONG>comand (<B><SPAN style="FONT-FAMILY: TimesNewRoman,Bold; mso-bidi-font-family: 'TimesNewRoman,Bold'">grompp<SPAN style="mso-spacerun: yes"> </SPAN>-f </SPAN></B><SPAN style="FONT-FAMILY: TimesNewRoman; mso-bidi-font-family: TimesNewRoman">pr.mdp </SPAN><B><SPAN style="FONT-FAMILY: TimesNewRoman,Bold;
mso-bidi-font-family: 'TimesNewRoman,Bold'">-c </SPAN></B><SPAN style="FONT-FAMILY: TimesNewRoman; mso-bidi-font-family: TimesNewRoman">trp_b4pr.pdb </SPAN><B><SPAN style="FONT-FAMILY: TimesNewRoman,Bold; mso-bidi-font-family: 'TimesNewRoman,Bold'">-p </SPAN></B><SPAN style="FONT-FAMILY: TimesNewRoman; mso-bidi-font-family: TimesNewRoman">trp.top </SPAN><B><SPAN style="FONT-FAMILY: TimesNewRoman,Bold; mso-bidi-font-family: 'TimesNewRoman,Bold'">-o </SPAN></B><SPAN style="FONT-FAMILY: TimesNewRoman; mso-bidi-font-family: TimesNewRoman">trp_pr.tpr)</SPAN>it gave that error message.</div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none">----------------------------------------------------------------------------------------</div> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none">File input/output
error:<BR>trp_b4pr.pdb<BR>----------------------------------------------------------------------------------------</SPAN></FONT></FONT></div> <div><BR>I have just checked the log file but there is no different error message.Only this;</div> <div> </div> <div>Range checking error:<BR>Explanation: During neighborsearching, we assign each particle to a grid<BR>based on its coordinates. If your system contains collisions or parameter<BR>errors that give particles very high velocities you might end up with some<BR>coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot<BR>put these on a grid, so this is usually where we detect those errors.<BR>Make sure your system is properly energy-minimized and that the potential<BR>energy seems reasonable before trying again.</div> <div>Variable ci has value -2147483648. It should have been within [ 0 .. 19488 ]<BR>Please report this to the mailing list (<A
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A>)</div> <div> </div> <div>----------------------------------------------------------------------------------------------------------------------------------</div> <div>Thanks very much again</div> <div>Sincerely</div> <div>Fulya<BR><BR><B><I>Tsjerk Wassenaar <tsjerkw@gmail.com></I></B> wrote:</div> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">Hi Fulya,<BR><BR>Did grompp give you any warnings? At what time did the error occur? At<BR>the start of the simulation or later? Could you check the log file for<BR>LINCS warnings, and try to track down the first occurrence? This would<BR>help to be able to say some more than "your system is exploding".<BR><BR>Best,<BR><BR>Tsjerk<BR><BR>On 3/27/07, fulya caglar <FULYACAGLAR@YAHOO.COM>wrote:<BR>><BR>><BR>> Note: forwarded message attached.<BR>><BR>> ________________________________<BR>>
Finding fabulous fares is fun.<BR>> Let Yahoo! FareChase search your favorite travel sites to find flight and<BR>> hotel bargains.<BR>><BR>> ---------- Forwarded message ----------<BR>> From: fulya caglar <FULYACAGLAR@YAHOO.COM><BR>> To: gmx-users-request@gromacs.org<BR>> Date: Mon, 26 Mar 2007 12:44:18 -0700 (PDT)<BR>> Subject: Drug - Enzyme Tutorial<BR>> Although I could run sucessfully speptide tutorial,while attempting the<BR>> drug-enzyme tutorial I am getting the following error message after the<BR>> first mdrun command ( mdrun -s trp_em.tpr -o trp_em.trr -c trp_b4pr.pdb -g<BR>> em.log –e em.edr);<BR>> -----------------------------------------<BR>> <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt; mso-layout-grid-align: none"> </div>><BR>> ---------------------------------------------------------------------------<BR>><BR>> I would be very glad to know why I get this type of error. Thanks very<BR>>
much.<BR>><BR>> With thanks<BR>> Sincerely Fulya<BR>><BR>><BR>> ________________________________<BR>> Food fight? Enjoy some healthy debate<BR>> in the Yahoo! Answers Food & Drink Q&A.<BR>><BR>><BR>> _______________________________________________<BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at http://www.gromacs.org/search before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the<BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read<BR>> http://www.gromacs.org/mailing_lists/users.php<BR>><BR><BR><BR>-- <BR>Tsjerk A. Wassenaar, Ph.D.<BR>Junior UD (post-doc)<BR>Biomolecular NMR, Bijvoet Center<BR>Utrecht University<BR>Padualaan 8<BR>3584 CH Utrecht<BR>The Netherlands<BR>P: +31-30-2539931<BR>F:
+31-30-2537623<BR>_______________________________________________<BR>gmx-users mailing list gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please search the archive at http://www.gromacs.org/search before posting!<BR>Please don't post (un)subscribe requests to the list. Use the<BR>www interface or send it to gmx-users-request@gromacs.org.<BR>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR></BLOCKQUOTE><BR><p> 
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