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On 29/02/2012 9:05 PM, aiswarya pawar wrote:
<blockquote
cite="mid:CAEa6cRDFM0A9r=YEAnBwVDFdOFs1PfYHMZq0Q0M7kybTXLBqWg@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
What makes you think there is only one atom satisfying that cutoff?<br>
<br>
<blockquote
cite="mid:CAEa6cRDFM0A9r=YEAnBwVDFdOFs1PfYHMZq0Q0M7kybTXLBqWg@mail.gmail.com"
type="cite"><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>
</blockquote>
<br>
Chunk of output from an unnamed file without giving the command line
that generated it is close to useless :-) Anyway, whatever
information is present here is not helping you observe the duration
of a contact between the protein and any given water molecule.<br>
<br>
<blockquote
cite="mid:CAEa6cRDFM0A9r=YEAnBwVDFdOFs1PfYHMZq0Q0M7kybTXLBqWg@mail.gmail.com"
type="cite"><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>
</blockquote>
<br>
If you have read g_dist -h and want to ask this question, then I did
not understand your previous statement of your objective.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAEa6cRDFM0A9r=YEAnBwVDFdOFs1PfYHMZq0Q0M7kybTXLBqWg@mail.gmail.com"
type="cite">
<br>
Thanks<br>
<br>
<div class="gmail_quote">On Wed, Feb 29, 2012 at 2:12 PM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
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
moz-do-not-send="true"
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 moz-do-not-send="true"
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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<br>
-- <br>
Aiswarya B Pawar<br>
<br>
<div> Project Assistant,<br>
Bioinformatics Dept, <br>
Indian Institute of Science<br>
Bangalore<br>
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<br clear="all">
<br>
-- <br>
Aiswarya B Pawar<br>
<br>
<div> Project Assistant,<br>
Bioinformatics Dept, <br>
Indian Institute of Science<br>
Bangalore<br>
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<br clear="all">
<br>
-- <br>
Aiswarya B Pawar<br>
<br>
<div>
Project Assistant,<br>
Bioinformatics Dept, <br>
Indian Institute of Science<br>
Bangalore<br>
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