Den 2019-07-31 kl. 15:00, skrev Omkar Singh:
I calculated these two vectors with Z-axis now I want to make
distribution plot p(costheeta) Vs cos(theeta). How can I plot because it is
giving the value only theeta. Is there any command.
Try write your own script.
Thanks
On Wed, Jul 31, 2019, 12:00 David van der Spoel <sp...@xray.bmc.uu.se>
wrote:
Den 2019-07-31 kl. 06:12, skrev Omkar Singh:
Thanks Sir,
I did like that only, Now how can I make the distribution plot for these
vectors. Eventhough I used "gmx analyze -f .xvg -dist .." command.
But
results is not proper. Can you suggest me regarding this?
Thank you
How about gmx gangle -oh ?
On Tue, Jul 30, 2019, 17:27 David van der Spoel <sp...@xray.bmc.uu.se>
wrote:
Den 2019-07-30 kl. 07:55, skrev Omkar Singh:
Hi,
I did by "gmx gangle ..." command. But I am not getting good result,
because I have a doubt in ndx file. Can you help me for making ndx
file.
How should I select the atom for vectors.
For OH it should be
1 2
1 3
4 5
4 6
7 8
7 9
etc., assuming a three particle water model with atoms O H H.
For HH it should be
2 3
5 6
8 9
etc.
A simple script would do it. The dipole vector is somewhat harder.
Thanks
On Mon, Jul 29, 2019, 22:50 David van der Spoel <sp...@xray.bmc.uu.se>
wrote:
Den 2019-07-29 kl. 18:26, skrev Omkar Singh:
Hi,
Meaning is that If I want to calculate angle between OH, HH and dip
vector
with positive Z-axis. How can I make index file for this issue? And
is
it
possible that the angle distribution of these vectors for bulk water
aproximatly linear. Hope now question is clear.
Probably. Check gmx gangle -g2 z
Thanks
On Mon, Jul 29, 2019, 16:33 David van der Spoel <
sp...@xray.bmc.uu.se>
wrote:
Den 2019-07-29 kl. 12:24, skrev Omkar Singh:
Hello everyone,
Is it possible that the probability distribution of HH, OH vector
for
bulk
water is approximately linear?
What do you mean?
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
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