Mark,<br><br>Right now am computing distance between each protein atom against all water atoms, which is taking too long for 5ns run. i cant reduce the frames either the number of water atoms. So is there any alternate.<br>
<br>Thanks<br><br><div class="gmail_quote">On Wed, Feb 29, 2012 at 12:27 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"><div class="im">
On 29/02/2012 5:17 PM, aiswarya pawar wrote:
<blockquote type="cite">Dear all,<br>
<br>
Am running g_mindist on large number of atoms, i would like to
know whether i can run this on more than one processors say 8
processors to speed up the task?</blockquote>
<br></div>
No. If it will take too long, you need to reduce your number of
frames (trjconv), or the number of atoms (also trjconv), or some
such.<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div class="im"><br>
<br>
<blockquote type="cite"> and will this effect the output in anyways.<br>
<br>
Thanks,<br clear="all">
<br>
-- <br>
Aiswarya B Pawar<br>
<br>
<br>
<br>
<fieldset></fieldset>
<br>
</blockquote>
<br>
</div></div>
<br>--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br></blockquote></div><br><br clear="all"><br>-- <br>Aiswarya B Pawar<br><br><div>
Project Assistant,<br>Bioinformatics Dept, <br>Indian Institute of Science<br>Bangalore<br><br></div><br>