<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Thanks Mark.<br><br><div>--<br>Sonali Dhindwal</div><br><br>--- On <b>Fri, 13/8/10, Mark Abraham <i><mark.abraham@anu.edu.au></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Mark Abraham <mark.abraham@anu.edu.au><br>Subject: Re: [gmx-users] Restarting the job<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Friday, 13 August, 2010, 8:46 AM<br><br><div id="yiv1271748233">----- Original Message -----<br>From: sonali dhindwal <sonali11dhindwal@yahoo.co.in><br>Date: Friday, August 13, 2010 0:59<br>Subject: [gmx-users] Restarting the job<br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br><br><table border="0" cellpadding="0" cellspacing="0"><tbody><tr><td style="font-family: inherit; font-style: inherit;
font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;" valign="top"><div id="yiv1271748233yiv1635197709"><table id="yiv1271748233yiv1635197709bodyDrftID" class="yiv1271748233yiv1635197709" border="0" cellpadding="0" cellspacing="0"><tbody><tr><td id="yiv1271748233yiv1635197709drftMsgContent" style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;"><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>Hello All,<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I have a query
regarding the restarts of the jobs after crash.<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I want to simulate a protein for 2 ns but in between due to system shutdown, it stopped, and I made a restart using this command:<br><pre><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>mdrun -s topol.tpr -cpi state.cpt -append</pre>now I checked the rmsd of in between by producing a .xtc file of the job which ran till now and then checked g_rms of the simulation, it is showing a graph like this,(I have attached in the mail)<br><br>See http://www.gromacs.org/Documentation/How-tos/Graphing_Data for a couple of gnuplot tips. I suspect the weirdness is gnuplot interpreting something as data that it should not interpret as data, and that the contents of the .xvg are actually the second half of normal RMS
variation.<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;"> </font><br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>this is showing rmsd after the point the job was restarted with some error in the beginning.<br><font style="font-style: normal; font-weight: normal; background-color: rgb(245, 248, 240); font-size: 14px;">> </font>I want to know if there will be error at the end of the job too in the output file, .gro ?<br></td></tr></tbody></table></div></td></tr></tbody></table><br>The final .gro will have the final coordinates, as normal.<br><br>Mark
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