On 29/02/2012 9:05 PM, aiswarya pawar wrote:
Mark,
In the g_mindist output data gives which atom was within cutoff to
protein atom ie the output file of g_mindist
What makes you think there is only one atom satisfying that cutoff?
5.000000e+02 518 42680
5.010000e+02 518 20942
5.020000e+02 518 67844
5.030000e+02 518 5984
5.040000e+02 518 67844
5.050000e+02 518 5984
5.060000e+02 518 30116
5.070000e+02 518 67844
5.080000e+02 518 32957
5.090000e+02 518 67844
5.100000e+02 518 19610
5.110000e+02 518 19610
5.120000e+02 518 22895
5.130000e+02 518 30116
5.140000e+02 518 19610
5.150000e+02 518 22895
5.160000e+02 518 13628
5.170000e+02 518 5984
2nd column is the protein atom and the 3rd column the water atom.
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.
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?
If you have read g_dist -h and want to ask this question, then I did not
understand your previous statement of your objective.
Mark
Thanks
On Wed, Feb 29, 2012 at 2:12 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 29/02/2012 7:21 PM, aiswarya pawar wrote:
Mark,
i want to know which water atoms stay within a cut off to protein
atom.
OK, but as you will read in g_mindist -h, it will count such atoms
and not identify which they were...
ie i need the duration at which a water resides on the protein atoms.
... 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.
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.
so for that i need the whole 5ns frames because am looking for
water molecules which reside more than 50% of time.
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?
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.
Mark
Thanks
On Wed, Feb 29, 2012 at 12:41 PM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> wrote:
On 29/02/2012 6:01 PM, aiswarya pawar wrote:
Mark,
Right now am computing distance between each protein atom
against all water atoms,
That's expensive. mdrun goes to great lengths to speed up
computing billions of distances.
which is taking too long for 5ns run. i cant reduce the frames
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.
either the number of water atoms. So is there any alternate.
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".
Mark
Thanks
On Wed, Feb 29, 2012 at 12:27 PM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>>
wrote:
On 29/02/2012 5:17 PM, aiswarya pawar wrote:
Dear all,
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?
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.
Mark
and will this effect the output in anyways.
Thanks,
--
Aiswarya B Pawar
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Indian Institute of Science
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Bioinformatics Dept,
Indian Institute of Science
Bangalore
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Bioinformatics Dept,
Indian Institute of Science
Bangalore
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