<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><br><br>--- On <b>Wed, 15/7/09, 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] Lincs Warning<br>To: "Discussion list for GROMACS users" <gmx-users@gromacs.org><br>Date: Wednesday, 15 July, 2009, 5:23 PM<br><br><div class="plainMail">Samik Bhattacharya wrote:<br>> Hi all, i ma simulating a membrane protein, in which i am facing a problem in the equilibration step. in the NVT equilibration when i am running the mdrun command i am getting a msg like<br>> <br>> Program mdrun, VERSION 4.0.5<br>> Source code file: constr.c, line: 136<br>> <br>> Fatal error:<br>> Too many LINCS warnings (1966)<br>> If you know what you are doing you can
adjust the lincs warning threshold in your mdp file<br>> or set the environment variable GMX_MAXCONSTRWARN to -1,<br>> but normally it is better to fix the problem<br>> i cant understand how to fix the problem.. where actually lies the error? is it in the mdp file i am using? some suggestions will be really helpful in this regard. Thank you all for the help in advance.<br><br><a href="http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings" target="_blank">http://oldwiki.gromacs.org/index.php/Errors#LINCS.2FSETTLE.2FSHAKE_warnings</a><br><br><br><br>Thanks You Mark. for your help... perhaps the error lies lies in EM step which converged very early in previous steps. when i was running EM for 5000 steps it was converging in less than 50 steps. and was showing a msg like<br><h2 style="font-weight: normal; font-family: times new roman,new york,times,serif;"><font size="4"><span class="mw-headline">Stepsize too small, or no
change in energy. Converged to machine precision, but not to the requested precision </span></font></h2><br>would doule precision remove this problem? again i cant rule out the system blowing up error. in that case how to increase 1-4 interaction?<br>looking forward for your valuable comments. Thank You<br>Shamik<br></div></blockquote></td></tr></table><br>
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