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On 31/01/2012 6:05 PM, Emanuel Birru wrote:
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<div style="direction: ltr; font-family: Tahoma; color: rgb(0, 0,
0); font-size: 10pt;">Yeah, Tsjerk is is right, it seems you are
using 4 cpu and your system is too small to run in on more than
one node (CPU).<br>
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<br>
If you look at the minimum required DD cell size reported by mdrun,
it is much too large (~4nm). It is quite likely that there is
problem other than simulation cell size.<br>
<br>
Mark<br>
<br>
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<div id="divRpF737569" style="direction: ltr; "><font
color="#000000" face="Tahoma" size="2"><b>From:</b>
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>
[<a class="moz-txt-link-abbreviated" href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>] on behalf of Tsjerk
Wassenaar [<a class="moz-txt-link-abbreviated" href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>]<br>
<b>Sent:</b> Tuesday, January 31, 2012 5:58 PM<br>
<b>To:</b> Discussion list for GROMACS users<br>
<b>Subject:</b> Re: [gmx-users] problem with energy
minimization<br>
</font><br>
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<p>Hi Anushree,</p>
<p>You're not using a single cpu, although you probably
think you do. Is this em in vacuum or just a small system?
Either way, you can enforce running on a single cpu by
adding '-nt 1' to the mdrun options.</p>
<p>Cheers,</p>
<p>Tsjerk</p>
<blockquote type="cite">On Jan 31, 2012 7:53 AM, "Anushree
Tripathi" <<a moz-do-not-send="true"
href="mailto:anushritripathi@gmail.com" target="_blank">anushritripathi@gmail.com</a>>
wrote:<br>
<br>
I am using single CPU for this simulation.<br>
<br>
<div class="gmail_quote">
<p><font color="#500050">On Tue, Jan 31, 2012 at 11:09
AM, Emanuel Birru <<a moz-do-not-send="true"
href="mailto:Emanuel.Birru@monash.edu"
target="_blank">Emanuel.Birru@monash.edu</a>>
wrote:
</font></p>
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<p><font color="#500050">> > > > From: <a
moz-do-not-send="true"
href="mailto:gmx-users-bounces@gromacs.org"
target="_blank">
gmx-users-bounces@gromacs.org</a> [mailto:<a
moz-do-not-send="true"
href="mailto:gmx-users-bounces@gromacs.org"
target="_blank">gmx-users-bounces@gromacs.org</a>]
On Behalf Of An...</font></p>
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