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<blockquote type=cite class=cite cite>I could solvate the protein and add
30 NA+ ions. But the MD run got<br>
crashed giving some errors which I am not able to debug. I am
attaching<br>
the ("full.mdp") parameter file and the message
("log") generated by<br>
mdrun. I'll be thankful if anyone of you can suggest me what to
do.</blockquote><br>
<a href="http://www.gromacs.org/search/index.php?query=LINCS+warning&max=20&result=normal&sort=score&idxname=gromacs_site&idxname=mailing_lists" eudora="autourl">http://www.gromacs.org/search/index.php?query=LINCS+warning&max=20&result=normal&sort=score&idxname=gromacs_site&idxname=mailing_lists</a><br><br>
That URL pulls up some threads on this list that deal with that sort of
error that you are seeing.<br><br>
I believe it can be either that the starting confirmation is not in a
stable enough state or pressure coupling is too tight.<br><br>
Catch ya,<br>
<x-sigsep><p></x-sigsep>
<b>Dr. Dallas Warren<br>
</b><i>Research Fellow<br>
</i>Department of Pharmaceutical Biology and Pharmacology<br>
Victorian College of Pharmacy, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<font color="#0000FF"><u>dallas.warren@vcp.monash.edu.au<br>
</u></font>+61 3 9903 9083<br>
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