Mark,<br><br>In the g_mindist output data gives which atom was within cutoff to protein atom ie the output file of g_mindist <br><br>5.000000e+02 518 42680<br>5.010000e+02 518 20942<br>5.020000e+02 518 67844<br>
5.030000e+02 518 5984<br>5.040000e+02 518 67844<br>5.050000e+02 518 5984<br>5.060000e+02 518 30116<br>5.070000e+02 518 67844<br>5.080000e+02 518 32957<br>
5.090000e+02 518 67844<br>5.100000e+02 518 19610<br>5.110000e+02 518 19610<br>5.120000e+02 518 22895<br>5.130000e+02 518 30116<br>5.140000e+02 518 19610<br>
5.150000e+02 518 22895<br>5.160000e+02 518 13628<br>5.170000e+02 518 5984<br><br>2nd column is the protein atom and the 3rd column the water atom.<br><br>if iam doing g_dist how is it possible to know the which water molecule has to be considered for the distance calculations ie should i compute the distance between one protein atom against all the water within the cut off individually?<br>
<br>Thanks<br><br><div class="gmail_quote">On Wed, Feb 29, 2012 at 2:12 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 7:21 PM, aiswarya pawar wrote:
</div><blockquote type="cite">Mark,<br>
<br><div class="im">
i want to know which water atoms stay within a cut off to protein
atom.</div></blockquote>
<br>
OK, but as you will read in g_mindist -h, it will count such atoms
and not identify which they were...<div class="im"><br>
<br>
<blockquote type="cite"> ie i need the duration at which a water resides on
the protein atoms.</blockquote>
<br></div>
... and identity of the atoms is needed for measuring duration of
contact. g_dist does something like this, and reading g_mindist -h
should have prompted you to find this out.<br>
<br>
Otherwise, you will have to construct an index group for each water
molecule, and script a loop to examine each water molecule
separately using some tool that observes what you really want to
measure.<div class="im"><br>
<br>
<blockquote type="cite"> so for that i need the whole 5ns frames because am
looking for water molecules which reside more than 50% of time.<br>
</blockquote>
<br></div>
You also need to be clear about whether you care about continuous
contact. Does a water molecule that oscillates at a distance around
the cutoff reside about 50% of the time?<br>
<br>
You still don't need high time resolution for testing whether this
analysis might give you the information you want. The water
molecules that are in contact for more than 50% of the time
(continuous or not) will show up in 5 snapsnots spaced every
nanosecond. 5000 snapshots every picosecond is better, but not if
you can't afford to wait for it.<div><div class="h5"><br>
<br>
Mark<br>
<br>
<blockquote type="cite">
<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" 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 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> <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><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><font color="#888888"><br>
<br>
Mark</font></span>
<div><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>
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Bioinformatics Dept, <br>
Indian Institute of Science<br>
Bangalore<br>
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