<div dir="ltr"><div>Yes, you are right. I made a mistake to write an error:</div><div><span lang="EN"></span> </div><div><span lang="EN">[n0017:07436] *** Process received signal ***</span></div><div>
[n0017:07436] Signal: Segmentation fault (11)</div><div>
[n0017:07436] Signal code: Address not mapped (1)</div><div>
[n0017:07436] Failing at address: 0x1d620d20</div><p> </p><p>What do you mean for "Better energy minimization"?</p><p> </p><p>Thanks,</p><p>Dariush </p><div> </div><div> </div><div><br><br></div><div class="gmail_quote">
On Wed, Mar 14, 2012 at 10:08 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid" class="gmail_quote">
<div class="im"><br>
<br>
Dariush Mohammadyani wrote:<br>
<blockquote style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid" class="gmail_quote">
Dear user,<br>
When I am using:<br>
genbox -cp confout.gro -cs water-1bar-303K.gro -vdwd 0.21 -o solvated.gro<br>
to add water in a coarse grained system, after running mdrun I am getting "Syntax error" and it shows maybe the distances are so close or there are some clashes.<br>
<br>
</blockquote>
<br></div>
I've never heard of mdrun throwing a syntax error. Can you please copy and paste the complete error message from your terminal?<div class="im"><br>
<br>
<blockquote style="margin:0px 0px 0px 0.8ex;padding-left:1ex;border-left-color:rgb(204,204,204);border-left-width:1px;border-left-style:solid" class="gmail_quote">
Do you know how can I figure it out?<br>
Or actually if we have some clashes in system how we can correct them?<br>
<br>
</blockquote>
<br></div>
Better energy minimization typically solves bad atomic clashes.<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" target="_blank" value="+15402319080">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
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