Re: [gmx-users] xmgrace graphs

[ram bio]

Thanks

On Wed, Oct 3, 2012 at 6:04 AM, Justin Lemkul  wrote:
>
>
> On 10/3/12 12:06 AM, naga sundar wrote:
>>
>> Dear Pramod
>>
>>   use the command
>>
>>   xmgrace  -nxy file1.xvg  file2.xvg
>>
>>   Instead of file1 and file2 use ur file name.
>>
>
> Distance plots produced by g_dist have four data sets (distance and x,y,z
> components) so plotting in this way can be quite messy.  Leave out the -nxy
> if you want to only plot the total distance and not the remaining (x,y,z)
> components.
>
> -Justin
>
>
>> On Tue, Oct 2, 2012 at 8:49 PM, ram bio  wrote:
>>
>>> Dear Gromacs users,
>>>
>>> I am trying to find inter atomic distances between ligand atoms and
>>> protein residues using Gromacs commands and could generate individual
>>> xvg files, but could not figure out how to merge or show all the xvg
>>> files in one graph using xmgrace.
>>>
>>> Cold you please suggest?
>>>
>>> Thanks and Regards,
>>>
>>> Pramod
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
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>>>
>>
>>
>>
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
>
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Re: [gmx-users] xmgrace graphs

[Justin Lemkul]

On 10/3/12 12:06 AM, naga sundar wrote:

Dear Pramod

  use the command

  xmgrace  -nxy file1.xvg  file2.xvg

  Instead of file1 and file2 use ur file name.



Distance plots produced by g_dist have four data sets (distance and x,y,z 
components) so plotting in this way can be quite messy.  Leave out the -nxy if 
you want to only plot the total distance and not the remaining (x,y,z) components.


-Justin


On Tue, Oct 2, 2012 at 8:49 PM, ram bio  wrote:


Dear Gromacs users,

I am trying to find inter atomic distances between ligand atoms and
protein residues using Gromacs commands and could generate individual
xvg files, but could not figure out how to merge or show all the xvg
files in one graph using xmgrace.

Cold you please suggest?

Thanks and Regards,

Pramod
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] xmgrace graphs

[naga sundar]

Dear Pramod

 use the command

 xmgrace  -nxy file1.xvg  file2.xvg

 Instead of file1 and file2 use ur file name.

On Tue, Oct 2, 2012 at 8:49 PM, ram bio  wrote:

> Dear Gromacs users,
>
> I am trying to find inter atomic distances between ligand atoms and
> protein residues using Gromacs commands and could generate individual
> xvg files, but could not figure out how to merge or show all the xvg
> files in one graph using xmgrace.
>
> Cold you please suggest?
>
> Thanks and Regards,
>
> Pramod
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>



-- 
Regards
N.NagaSundaram
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[gmx-users] xmgrace graphs

[ram bio]

Dear Gromacs users,

I am trying to find inter atomic distances between ligand atoms and
protein residues using Gromacs commands and could generate individual
xvg files, but could not figure out how to merge or show all the xvg
files in one graph using xmgrace.

Cold you please suggest?

Thanks and Regards,

Pramod
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Re: [gmx-users] xmgrace-plotting of g_sas output (averages+standarddeviation)

[Justin A. Lemkul]

On 5/30/12 7:47 AM, Marc Hömberger wrote:

Hi,

when I try the mentioned method for the GROMACs output (xvg file, supposedly
formatted for use with xmgrace) I am unable to print the standarddeviation. I f
I select the XYDY method it just ignores it and plots again an XY graph.

What I then did: I stripped the file so that only residue number (column 1),
average (column 2) and the standarddeviation (column 3) are in the file (each
comma seperated by a single space). When i open that in xmgrace and I select the
XYDY set it is displayed correctly.
However, this means I have to strip each file. Is there any way I can circumvent
stripping every single file?



Remove or comment out the "@TYPE xy" line.

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] xmgrace-plotting of g_sas output (averages+standarddeviation)

[Marc Hömberger]

Hi,

when I try the mentioned method for the GROMACs output (xvg file,
supposedly formatted for use with xmgrace) I am unable to print the
standarddeviation. I f I select the XYDY method it just ignores it and
plots again an XY graph.

What I then did: I stripped the file so that only residue number (column
1), average (column 2) and the standarddeviation (column 3) are in the file
(each comma seperated by a single space). When i open that in xmgrace and I
select the XYDY set it is displayed correctly.
However, this means I have to strip each file. Is there any way I can
circumvent stripping every single file?

Best
Marc

On Wed, May 30, 2012 at 6:22 AM, Justin A. Lemkul  wrote:

>
>
> On 5/30/12 4:58 AM, Marc Hömberger wrote:
>
>> Hello,
>>
>> I am currently analyzing a bunch of trajectories and one thing I am doing
>> is to
>> use g_sas to generate the average and standard deviation per residue. The
>> resulting xvg file should be formatted for use with xmgrace but I do not
>> seem to
>> be able to get the standard deviation in the graph. I tried searching for
>> some
>> hints and also looked through xmgrace's manual but there was nothing
>> about file
>> format where the second column is the standardeviation and how to show
>> that in
>> the graph. Can anyone of you maybe point me in the right direction on how
>> to
>> plot the averages plus the corresponding standard deviation?
>>
>>
> In the window for importing data, choose "XYDY" from the "Set type"
> dropdown menu.
>
> -Justin
>
>
> --
> ==**==
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin
>
> ==**==
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Re: [gmx-users] xmgrace-plotting of g_sas output (averages+standarddeviation)

[Justin A. Lemkul]

On 5/30/12 4:58 AM, Marc Hömberger wrote:

Hello,

I am currently analyzing a bunch of trajectories and one thing I am doing is to
use g_sas to generate the average and standard deviation per residue. The
resulting xvg file should be formatted for use with xmgrace but I do not seem to
be able to get the standard deviation in the graph. I tried searching for some
hints and also looked through xmgrace's manual but there was nothing about file
format where the second column is the standardeviation and how to show that in
the graph. Can anyone of you maybe point me in the right direction on how to
plot the averages plus the corresponding standard deviation?



In the window for importing data, choose "XYDY" from the "Set type" dropdown 
menu.

-Justin


--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] xmgrace-plotting of g_sas output (averages+standarddeviation)

[Marc Hömberger]

Hello,

I am currently analyzing a bunch of trajectories and one thing I am doing
is to use g_sas to generate the average and standard deviation per residue.
The resulting xvg file should be formatted for use with xmgrace but I do
not seem to be able to get the standard deviation in the graph. I tried
searching for some hints and also looked through xmgrace's manual but there
was nothing about file format where the second column is the
standardeviation and how to show that in the graph. Can anyone of you maybe
point me in the right direction on how to plot the averages plus the
corresponding standard deviation?

Best
Marc
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Re: [gmx-users] xmgrace

[Jussi Lehtola]

On Fri, 8 Jul 2011 13:07:56 +0530
manoj gadhwal  wrote:

> Hello to all,
>I am using the Gromacs 4.5.3 in Centos-5 and I
> need the xmgrace or Grace for plotting the graph for output file .
> But when I tried to install grace by the option *'yum install
> grace*', there was no file to install. and I am not able to install
> properly by the grace tar.gz file. So can anyone tell me the the
> compatibility file and process of grace installation.
> 
> Thanks in advance.
> 

Enable the Fedora EPEL repository with 

# rpm -Uvh \
http://download.fedoraproject.org/pub/epel/5/i386/epel-release-5-4.noarch.rpm

after which you can install grace with

# yum -y install grace
-- 

Mr. Jussi Lehtola, M. Sc. Doctoral Student
jussi.leht...@helsinki.fi Department of Physics
http://www.helsinki.fi/~jzlehtol  University of Helsinki
Office phone: +358 9 191 50 632   Finland

Jussi Lehtola, FM Tohtorikoulutettava
jussi.leht...@helsinki.fi Fysiikan laitos
http://www.helsinki.fi/~jzlehtol  Helsingin Yliopisto
Työpuhelin: (0)9 191 50 632

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Re: [gmx-users] xmgrace

[Mark Abraham]

On 8/07/2011 5:37 PM, manoj gadhwal wrote:

Hello to all,
   I am using the Gromacs 4.5.3 in Centos-5 and I need 
the xmgrace or Grace for plotting the graph for output file . But when 
I tried to install grace by the option */'yum install grace/*', there 
was no file to install. and I am not able to install properly by the 
grace tar.gz file. So can anyone tell me the the compatibility file 
and process of grace installation.


Google does know quite a bit about these things :-)

Mark
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[gmx-users] xmgrace

[manoj gadhwal]

Hello to all,
   I am using the Gromacs 4.5.3 in Centos-5 and I need the
xmgrace or Grace for plotting the graph for output file . But when I tried
to install grace by the option *'yum install grace*', there was no file to
install. and I am not able to install properly by the grace tar.gz file. So
can anyone tell me the the compatibility file and process of grace
installation.

Thanks in advance.

-- 
Manoj Kumar Gadhwal (M. Pharma),
Research Schloar,
Prin. K. M. Kundnani College of Pharmacy,
Colaba, Mumbai-05.
Cont. No. +91 9769051866
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Re: [gmx-users] xmgrace

[Oliver Grant]

Command is xmgrace and it needs to be in your $PATH.

On 13 May 2010 12:19, shahid nayeem  wrote:

> Dear all
> I downloaded xmgr-4.1.2.tar.gz and tried to install by following commands.
> tar -xvzf xmgr-4.1.2.tar.gz
> cd xmgr-4.1.2
> ./configure
> make
> make install
> But it gives error command xmgr not found.
> Please help.
> shahid Nayeem
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[gmx-users] xmgrace

[shahid nayeem]

Dear all
I downloaded xmgr-4.1.2.tar.gz and tried to install by following commands.
tar -xvzf xmgr-4.1.2.tar.gz
cd xmgr-4.1.2
./configure
make
make install
But it gives error command xmgr not found.
Please help.
shahid Nayeem
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Re: [gmx-users] xmgrace plot

[Justin A. Lemkul]

Henry Yang wrote:

Hello Jon,

Thnx. One more question. I have the output of every 10 ns simulation 
over 50 ns. For every 10 ns simulation step I have the .xvg file . Is 
there any way in xmgrace so that I can concatenate all the .xvg file 
from 0 to 50 ns simulation and show them one xmgrace graph

Thanks again


It is probably easier to simply concatenate your trajectory files (trjcat) 
and/or energy files (eneconv) so you don't have to worry about running multiple 
commands, concatenating all the output of every analysis, and dealing with 
duplicate start/end times.


-Justin



Henry


*From:* Jon Fuller 
*To:* Discussion list for GROMACS users 
*Sent:* Tue, December 8, 2009 11:53:25 AM
*Subject:* Re: [gmx-users] xmgrace plot

 >From the command line you can type xmgrace file1.xvg file2.xvg (where 
file1 and file2 are the filenames!).


Jon

2009/12/8 Henry Yang mailto:henryy...@yahoo.com>>

Hello everyone,

I am also new to xmgrace. I have two .xvg file which I have got from
the simulation data analysis.  How can I open both of them in one
xmgrace graph with two distinct color? How can I proceed with the
comand?

I know this is very basic but I have to learn!
Pls give me response.

Henry
Biochemistry



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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] xmgrace plot

[Henry Yang]

Hello Jon,

Thnx. One more question. I have the output of every 10 ns simulation over 50 
ns. For every 10 ns simulation step I have the .xvg file . Is there any way in 
xmgrace so that I can concatenate all the .xvg file from 0 to 50 ns simulation 
and show them one xmgrace graph
Thanks again

Henry





From: Jon Fuller 
To: Discussion list for GROMACS users 
Sent: Tue, December 8, 2009 11:53:25 AM
Subject: Re: [gmx-users] xmgrace plot

>From the command line you can type xmgrace file1.xvg file2.xvg (where file1 
>and file2 are the filenames!).

Jon


2009/12/8 Henry Yang 

Hello everyone,
>
>I am also new to xmgrace. I have two .xvg file which I have got from the 
>simulation data analysis.  How can I open both of them in one xmgrace graph 
>with two distinct color? How can I proceed with the comand? 
>
>I know this is very basic but I have to learn!
>Pls give me response.
>
>Henry
>Biochemistry
>
>
>
>--
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Re: [gmx-users] xmgrace plot

[Jon Fuller]

>From the command line you can type xmgrace file1.xvg file2.xvg (where file1
and file2 are the filenames!).

Jon

2009/12/8 Henry Yang 

> Hello everyone,
>
> I am also new to xmgrace. I have two .xvg file which I have got from the
> simulation data analysis.  How can I open both of them in one xmgrace graph
> with two distinct color? How can I proceed with the comand?
>
> I know this is very basic but I have to learn!
> Pls give me response.
>
> Henry
> Biochemistry
>
>
>
> --
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[gmx-users] xmgrace plot

[Henry Yang]

Hello everyone,

I am also new to xmgrace. I have two .xvg file which I have got from the 
simulation data analysis.  How can I open both of them in one xmgrace graph 
with two distinct color? How can I proceed with the comand? 

I know this is very basic but I have to learn!
Pls give me response.

Henry
Biochemistry


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Re: [gmx-users] xmgrace

[Justin A. Lemkul]

pawan raghav wrote:

While running MD simulation I have number of queries mentioned below:
 
1. When executing xmgrace command it returns the bash command not found, 
then how to install GRACE package on windows?


Visit the Grace website and follow whatever download and installation 
instructions they provide.


2. When defining the box dimention then how do I know about the distance 
of protein (207 residues) from the box wall should be greater than half 
of the Cut-Off (1.4nm)?


I don't fully understand this question.  The longest cutoff must be shorter than 
half the shortest box vector to satisfy the minimum image convention.  This is 
usually accomplished by setting a reasonable value of -d when using editconf, 
checking the box vectors that result and setting cutoffs appropriate for the 
force field of interest.


3. In fullmd_sol.mdp file how to find the time step value because I 
don't have confirmation about that.


You specify time step with the dt parameter.

4. When using grommp command to generate fullmd.tpr file, it will shows 
3 notes 
(a.) The Berendsen thermostat does not 
generate the correct K.E distribution, and suggesting to use v- rescale 
thermostat


Good suggestion.  There's lots of literature on the topic.

(b.) Why the system has non-zero total 
charge : -2.01e+00
(c.) [file fullmd_sol.mdp, line unknow]: you 
are using a plain coulomb cut-off, which might produce artifacts. You 
might want to consider using PME   electostatics.


For (b) and (c), it sounds like you need to do some tutorials and background 
reading.  Might I suggest:


http://www.gromacs.org/Documentation/Tutorials


5. How to save screen of cygwin (general question)
 


Copy and paste from the command line?  There's a screenshot mechanism somewhere 
in Windows otherwise.


-Justin


Please solve these problems if you can I am thankful to you.

--
Pawan



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] xmgrace

[pawan raghav]

While running MD simulation I have number of queries mentioned below:

1. When executing xmgrace command it returns the bash command not found,
then how to install GRACE package on windows?
2. When defining the box dimention then how do I know about the distance of
protein (207 residues) from the box wall should be greater than half of the
Cut-Off (1.4nm)?
3. In fullmd_sol.mdp file how to find the time step value because I don't
have confirmation about that.
4. When using grommp command to generate fullmd.tpr file, it will shows 3
notes
(a.) The Berendsen thermostat does not generate
the correct K.E distribution, and suggesting to use v- rescale thermostat
(b.) Why the system has non-zero total charge :
-2.01e+00
(c.) [file fullmd_sol.mdp, line unknow]: you are
using a plain coulomb cut-off, which might produce artifacts. You might want
to consider using PME   electostatics.
5. How to save screen of cygwin (general question)

Please solve these problems if you can I am thankful to you.

-- 
Pawan
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Re: [gmx-users] xmgrace

[Florian Haberl]

Hi,

On Thursday, 3. May 2007 22:07, Michal Walczak wrote:
> Dear Gromacs users,
>
> I'd like to ask if anyone could tell me how to open *.rms file in xmgrace,
> if it's possible of course or how to convert such a file into *.xvg? That
> *.rms file is an output from NWChem.

open it with your favourite text editor, if its ascii you can use xmgrace for 
making plots, also gnuplot will work. These programms can open any file 
extensions.


>
> Best wishes,
>
> Michal Walczak


Grettings,

Florian

-- 
---
 Florian Haberl
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone: +49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de
---
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Re: [gmx-users] xmgrace

[Mark Abraham]

Michal Walczak wrote:

Dear Gromacs users,

I'd like to ask if anyone could tell me how to open *.rms file in 
xmgrace, if it's possible of course or how to convert such a file into 
*.xvg? That *.rms file is an output from NWChem.


Are the xmgrace or NWChem mailing lists the right places to be asking 
this question? The answer is going to depend on knowing the file format 
of an .rms file, which doesn't have anything to do with gromacs :-)


Mark
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[gmx-users] xmgrace

[Michal Walczak]

Dear Gromacs users,

I'd like to ask if anyone could tell me how to open *.rms file in xmgrace,
if it's possible of course or how to convert such a file into *.xvg? That
*.rms file is an output from NWChem.

Best wishes,

Michal Walczak
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