Mark,<br><br>i want to know which water atoms stay within a cut off to protein atom. ie i need the duration at which a water resides on the protein atoms. so for that i need the whole 5ns frames because am looking for water molecules which reside more than 50% of time.<br>
<br>Thanks<br><br><div class="gmail_quote">On Wed, Feb 29, 2012 at 12:41 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 6:01 PM, aiswarya pawar wrote:
<blockquote type="cite">Mark,<br>
<br>
Right now am computing distance between each protein atom against
all water atoms,</blockquote>
<br></div>
That's expensive. mdrun goes to great lengths to speed up computing
billions of distances. <br><div class="im">
<br>
<blockquote type="cite"> which is taking too long for 5ns run. i cant reduce
the frames</blockquote>
<br></div>
Yes you can. Even if you think you need data from every frame, you
probably don't because they're correlated with each other, and at
the very least you can do a pilot study on a frame every 100ps or
every nanosecond before committing to one on all the frames.<div class="im"><br>
<br>
<blockquote type="cite"> either the number of water atoms. So is there any
alternate.<br>
<br>
</blockquote>
<br></div>
You are not likely to get a better solution if you only describe
your attempt, rather than describe the objective. Asking "how do I
hammer harder?" if you're hammering a screw makes it impossible to
get the correct solution "Use a screwdriver".<span class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span><div class="im"><br>
<br>
<blockquote type="cite">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" target="_blank">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> 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><font color="#888888"><br>
<br>
Mark</font></span>
<div><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>
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-- <br>
Aiswarya B Pawar<br>
<br>
<div>
Project Assistant,<br>
Bioinformatics Dept, <br>
Indian Institute of Science<br>
Bangalore<br>
<br>
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Project Assistant,<br>Bioinformatics Dept, <br>Indian Institute of Science<br>Bangalore<br><br></div><br>