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On 25/01/2012 9:32 PM, Anushree Tripathi wrote:
<blockquote
cite="mid:CAAx43BxTLSgjJX_pmHrRbCqEabNov18wH+H1m3_THRxA+_DJhw@mail.gmail.com"
type="cite">I have used "mdrun -v deffnm em" command for energy
minimization just after running the command i.e., given below:<br>
<font size="3"><font face="Arial"><br>
</font></font>perl <a moz-do-not-send="true"
href="http://inflategro.pl">inflategro.pl</a> system.gro 4 DPPC
14 system_inflated.gro 5 area.dat<br>
But When I run the command which is given below:<br>
<font face="Arial"><font size="3">Eeeeek! No confout.gro at all!<br>
<br>
Died at <a moz-do-not-send="true" href="http://inflategro.pl">inflategro.pl</a>
line 81.<br>
<br>
Please guide me to troubleshoot the error.<br>
Also clarify the lines given in tutorial "</font></font><font
face="Arial"><font size="3">Note how many lipids were deleted
and update the <code>[ molecules ]</code> directive of your
topology accordingly. Run energy minimization. Then, scale
down the lipids by a factor of 0.95 (assuming you have used
default names, the result of the minimization is called
"confout.gro"):".</font></font><br>
</blockquote>
<br>
Apparently you did the EM too late, or it broke. Check the order of
your operations and pay attention to warnings and errors.<br>
<br>
Mark<br>
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