Re: [gmx-users] Tetrahedral Order Parameter

[Dallas Warren]

I can't provide advice directly, but more generally ... try things out,
experiment. All it takes is a bit of time and it will help you get a better
understanding of how things work. Plus you will get further faster doing it
yourself, rather than waiting a day or two for someone else to respond with
some help, which may or may not be exactly what you are after. If you still
can't figure it out, post exactly what you have done, what the output was,
how it deviated from what expected etc.

Plus you should be able to find a few instances of others using the command
via a web search.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Thu, 19 Sep 2019 at 06:36, m g  wrote:

> Dear Justi,I want to calculate the Tetrahedral Order Parameter (Q) for
> water in my simulation system. I used "gmx hydorder" command but it is not
> clear for me. what kinds of flag must be use exactly? how can I set correct
> number for "-sgang1 and -sgang2" flags? This command is very confusing. how
> can I get Q?Thanks,Sana
> --
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[gmx-users] Tetrahedral Order Parameter

[m g]

Dear Justi,I want to calculate the Tetrahedral Order Parameter (Q) for water in 
my simulation system. I used "gmx hydorder" command but it is not clear for me. 
what kinds of flag must be use exactly? how can I set correct number for 
"-sgang1 and -sgang2" flags? This command is very confusing. how can I get 
Q?Thanks,Sana
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Re: [gmx-users] Tetrahedral order parameter

[Justin Lemkul]

On 8/20/19 7:51 AM, Omkar Singh wrote:

Hello gromacs users,
I am working on protein-water system.  I am trying to calculate
top(tetrahedral order parameter) by "gmx hydorder" command. After finding
xpm how to proceed for xvg format.


gmx hydorder does not produce such output. You may want to look into 
other optional output files like -or for raw data output, but I have no 
idea what is in that file or if it is what you need.


-Justin

--
==

Justin A. Lemkul, Ph.D.
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Office: 301 Fralin Hall
Lab: 303 Engel Hall

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[gmx-users] Tetrahedral order parameter

[Omkar Singh]

Hello gromacs users,
I am working on protein-water system.  I am trying to calculate
top(tetrahedral order parameter) by "gmx hydorder" command. After finding
xpm how to proceed for xvg format.

Thanks
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Re: [gmx-users] Tetrahedral order parameter

[Dallas Warren]

http://manual.gromacs.org/documentation/current/onlinehelp/gmx-hydorder.html

Recommend anyone looking for a way to calculate something, first go through
the documentation for the available scripts with GROMACS, lot of things
available there.
http://manual.gromacs.org/documentation/current/user-guide/cmdline.html#commands-by-name

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
-
When the only tool you own is a hammer, every problem begins to resemble a
nail.


On Fri, 2 Aug 2019 at 15:36, Omkar Singh  wrote:

> Hi all gmx-users,
> I have a water-protein simulated  system. I  want to calculate the
> Tetrahedral order parameter. Can anybody help me regarding this issue.
>
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[gmx-users] Tetrahedral order parameter

[Omkar Singh]

Hi all gmx-users,
I have a water-protein simulated  system. I  want to calculate the
Tetrahedral order parameter. Can anybody help me regarding this issue.


On Thu, Aug 1, 2019, 00:52 David van der Spoel  wrote:

> 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 
> > 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 
> >>> 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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> >>
> >>
> >> --
> >> 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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> 
> >>
> >>
> >> --
> >> 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.
> >> 

Re: [gmx-users] tetrahedral order parameter

[ISHRAT JAHAN]

I have used gmx hydorder but unable to understand the output as it gives
two .xpm and two .out file. what these file describe please help.

On Thu, Jun 1, 2017 at 6:14 PM, Justin Lemkul  wrote:

>
>
> On 6/1/17 3:42 AM, ISHRAT JAHAN wrote:
>
>> Dear all,
>> I want to calculate tetrahedral order parameter of water molecule.can
>> anyone tell me how to calculate it.
>>
>
> Use gmx hydorder
>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
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> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [gmx-users] tetrahedral order parameter

[Justin Lemkul]

On 6/1/17 3:42 AM, ISHRAT JAHAN wrote:

Dear all,
I want to calculate tetrahedral order parameter of water molecule.can
anyone tell me how to calculate it.


Use gmx hydorder

-Justin

--
==

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] tetrahedral order parameter

[ISHRAT JAHAN]

Dear all,
I want to calculate tetrahedral order parameter of water molecule.can
anyone tell me how to calculate it.
Thanks in advance
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