<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Abdul,<div><br></div><div>please keep Gromacs-related questions on the list. The error</div><div>is exactly as printed: You have more than 128 backups of md.log</div><div>in your directory, at this point mdrun does not make more backups</div><div>of md.log any more. You have to delete the #md.log.*# files.</div><div><br></div><div>Carsten</div><div><br></div><div><br><div><div><div>On Jun 18, 2010, at 7:24 AM, abdul wadood wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; ">Dear Carsten<br><br>When I reduce the number of steps in mdp file the error change which now<br><br>0: Fatal error:<br>0: Won't make more than 128 backups of md.log for you<br>0: -------------------------------------------------------<br>0:<br>0: "I Wonder, Should I Get Up..." (J0: p0_27074: p4_error: : -1<br>. Lennon)<br>0:<br>0: Halting program mdrun_mpi<br>0:<br>0: gcq#46: "I Wonder, Should I Get Up..." (J. Lennon)<br>0:<br>0: [0] MPI Abort by user Aborting program !<br>0: [0] Aborting program!<br>0: p4_error: latest msg from perror: No such file or directory<br><br><br><div>Abdul Wadood,<span class="Apple-converted-space"> </span><br>Research Scholar,<span class="Apple-converted-space"> </span><br>Dr.Panjwani Center for Molecular Medicine and<span class="Apple-converted-space"> </span><br>Drug Research,<span class="Apple-converted-space"> </span><br>International Center for Chemical and<span class="Apple-converted-space"> </span><br>Biological Science,<span class="Apple-converted-space"> </span><br>University of Karachi, Karachi-75720, Pakistan.<span class="Apple-converted-space"> </span><br>Email:<a href="mailto:wadoodbiochemist@hotmail.com">wadoodbiochemist@hotmail.com</a><span class="Apple-converted-space"> </span><br></div><br><br><br><br><hr id="stopSpelling">From:<span class="Apple-converted-space"> </span><a href="mailto:ckutzne@gwdg.de">ckutzne@gwdg.de</a><br>Subject: Re: Parallel instalation: gmx-users Digest, Vol 74, Issue 76<br>Date: Thu, 17 Jun 2010 16:36:51 +0200<br>To:<span class="Apple-converted-space"> </span><a href="mailto:wadoodbiochemist@hotmail.com">wadoodbiochemist@hotmail.com</a><br><br><div><div>On Jun 17, 2010, at 3:57 PM, abdul wadood wrote:</div><br class="ecxApple-interchange-newline"><blockquote><span class="ecxApple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; font-size: medium; "><div class="ecxhmmessage" style="font-size: 10pt; font-family: Verdana; ">Dear Carsten<br><br>I give the path for the topol.tpr file now the error is change which is<br><br>Fatal error:<br>3: Too many LINCS warnings (4254)<br>3: If you know what you are doing you can adjust the lincs warning threshold in your mdp file<br>3: or set the environment variable GMX_MAXCONSTRWARN to -1,<br>3: but normally it is better to fix the problem<br>3: -------------------------------------------------------<br>3:</div></span></blockquote>Maybe your system is not well equilibrated, or your time step is too long.</div><div><br></div><div>Carsten</div><br><hr>Hotmail is redefining busy with tools for the New Busy. Get more from your inbox.<span class="Apple-converted-space"> </span><a href="http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_2" target="_new">See how.</a></div></span></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 14px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br class="Apple-interchange-newline">--</div><div>Dr. Carsten Kutzner</div><div>Max Planck Institute for Biophysical Chemistry</div><div>Theoretical and Computational Biophysics</div><div>Am Fassberg 11, 37077 Goettingen, Germany</div><div>Tel. +49-551-2012313, Fax: +49-551-2012302</div><div><a href="http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne">http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne</a></div><div><br></div></div><br class="Apple-interchange-newline"></span><br class="Apple-interchange-newline"></span>
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