Re: [gmx-users] Coordination number

[Venkat Reddy]

Sir

Thank you for the reply. The higher graph is also broader and I thought
should then give a higher coordination number. Does gromacs use the box
density? does it not use 4*pi*r2*g(r) for calculating rdf (thats what I
read in a paper where the authors have used gromacs for simulation and
analyses)?where is the density coming then?

Thank you


On Wed, Aug 21, 2013 at 4:20 AM, Dallas Warren wrote:

> Peak can be higher, but if it is narrower the total area can still be
> less.  Remember it is an area under the curve.  Additionally, that overall
> system / box density that you are using may be different too, so that will
> make a difference.
>
> Catch ya,
>
> Dr. Dallas Warren
> Drug Discovery Biology
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3052
> dallas.war...@monash.edu
> +61 3 9903 9304
> -
> When the only tool you own is a hammer, every problem begins to resemble a
> nail.
>
> > -Original Message-
> > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> > boun...@gromacs.org] On Behalf Of Venkat Reddy
> > Sent: Monday, 19 August 2013 8:11 PM
> > To: Discussion list for GROMACS users
> > Subject: [gmx-users] Coordination number
> >
> > Dear Gromacs Users,
> >
> > I have a query about the g_rdf utility. I have two different systems of
> > water with Ionic Liquid 1 and Ionic Liquid 2. When I plot the rdf using
> >
> > g_rdf -f x_gro.pdb -s x.pdb -n rdf.ndx -o rdf1.xvg/rdf2.xvg -cn
> > rdf1_cn.xvg/rdf2_cn.xvg -rdf res_com
> >
> > where rdf1/rdf2 is for water distribution around Ionic liquid 1/2,
> >
> > the rdf1.xvg clearly shows a higher first peak g(r) than the rdf2.xvg.
> > Both
> > also have minima at the same distance. However, the coordination number
> > at
> > first minima from rdf1_cn.xvg is lesser than the same from rd2_cn.xvg.
> > How
> > is this possible? If the peak is larger, the integration of it should
> > give
> > a higher value right?
> >
> > Please help.
> >
> >
> > --
> > With Best Wishes
> > Venkat Reddy Chirasani
> > PhD student
> > Laboratory of Computational Biophysics
> > Department of Biotechnology
> > IIT Madras
> > Chennai
> > INDIA-600036
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] g_hydorder error

[Nidhi Katyal]

Dear all,

I am using following command in gromacs version 4.5.5:
g_hydorder -f *.xtc -s *.tpr -n *.ndx -o file1.xpm file2.xpm
But getting following error:
Internal error in pbc_dx, set_pbc has not been called

In my mdp file, I have set pbc to xyz

I have searched the archive and found that similar issue was raised earlier
in the past and was filed as a bug. I have seen bugzilla and found the
status to be closed.

Please help me resolve the problem. Any help is appreciated
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] g_hydorder error

[Justin Lemkul]

On 8/26/13 8:27 AM, Nidhi Katyal wrote:

Dear all,

I am using following command in gromacs version 4.5.5:
g_hydorder -f *.xtc -s *.tpr -n *.ndx -o file1.xpm file2.xpm
But getting following error:
Internal error in pbc_dx, set_pbc has not been called

In my mdp file, I have set pbc to xyz

I have searched the archive and found that similar issue was raised earlier
in the past and was filed as a bug. I have seen bugzilla and found the
status to be closed.

Please help me resolve the problem. Any help is appreciated



Upgrade to 4.6.3 and try again.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Gromacs 4.6.3 Installation Issues,

[HANNIBAL LECTER]

probably u do not have CUDA. If you are not really interested in performing
simulations using GPU, you can set -DGMX_GPU=off during cmake


On Sat, Aug 24, 2013 at 12:15 PM, No One  wrote:

> hi,
>
> i'm having difficulties installing gromacs by creating static links to the
> libraries for fftw3.
>
> i am currently running:
> cygwin1.7.24-1
> cmake2.8.11.2-1
> fftw33.3.3-1
>
> this is the input that i'm attempting to utilize and flags errors (and
> some combination there of):
> cmake FFTW3F_INCLUDE_DIR=C:\FFTW\fftw-3.3.3\api
>  FFTWF_LIBRARIES=C:\FFTW\fftw-3.3.3\.libs
>
> this is my error output:
> /cygdrive/c/gromacs/gromacs-4.6.3/build-cmake
> $ cmake FFTW3F_INCLUDE_DIR=C:\FFTW\fftw-3.3.3\api
>  FFTWF_LIBRARIES=C:\FFTW\fftw-3.3.3\.libs ..
> -- Could NOT find CUDA (missing:  CUDA_CUDART_LIBRARY) (found suitable
> version "5.5", minimum required is "3.2")
> -- Enabling native GPU acceleration
> CMake Error at cmake/FindFFTW.cmake:122 (message):
>   The FFTW library /usr/local/lib/libfftw3f.a cannot be used with shared
>   libraries.  Provide a different FFTW library by setting FFTWF_LIBRARY.
>  If
>   you don't have a different one, recompile FFTW with "--enable-shared" or
>   "--with-pic".  Or disable shared libraries for Gromacs by setting
>   BUILD_SHARED_LIBS to "no".  Note: Disabling shared libraries requires up
> to
>   10x as much disk space.
> Call Stack (most recent call first):
>   CMakeLists.txt:948 (find_package)
>
> any assistance would be appreciated. thanks.
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] error with g_dist

[chinnu657]

Hello all, I am trying to find the distance between 2 centres of mass using
g_dist.

I use the command:  g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n
index.ndx

but i get the error:
Fatal error:
Molecule in topology has atom numbers below and above natoms (1707).
You are probably trying to use a trajectory which does not match the first
1707 atoms of the run input file.
You can make a matching run input file with tpbconv.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
 
I tried using tpbconv like suggested. But that did not help. I really need
help on this as my submission deadline is getting closer and this is the
last simulation I need..

Thank you so much in advance

Chinnu




--
View this message in context: 
http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] error with g_dist

[Justin Lemkul]

On 8/26/13 4:05 PM, chinnu657 wrote:

Hello all, I am trying to find the distance between 2 centres of mass using
g_dist.

I use the command:  g_dist -s md_0_1.tpr -f md_0_1.xtc -o dist.xvg -n
index.ndx

but i get the error:
Fatal error:
Molecule in topology has atom numbers below and above natoms (1707).
You are probably trying to use a trajectory which does not match the first
1707 atoms of the run input file.
You can make a matching run input file with tpbconv.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I tried using tpbconv like suggested. But that did not help. I really need
help on this as my submission deadline is getting closer and this is the
last simulation I need..



The most likely explanation is that you did not save groups correctly using 
xtc-grps in the .mdp file.  In the absence of a description of what you're 
trying to measure, the contents of the index groups, and the gmxcheck output on 
the .xtc file, there's little anyone can do to help.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: error with g_dist

[chinnu657]

I'm basically trying to see how the distance between the ligand and protein
changes with time using their centres of mass and the only way I've come
across is by using g_dist.

I'm pasting the contents from the terminal after the doing a gmxcheck on the
md_0_1.xtc file which is my .xtc file from the production simulation.

Checking file md_0_1.xtc
Reading frame   0 time0.000  
# Atoms  33037
Precision 0.001 (nm)
Last frame   1000 time 2000.000  


Item#frames Timestep (ps)
Step  10012
Time  10012
Lambda   0
Coords10012
Velocities   0
Forces   0
Box   10012

can I attach the index.ndx file again? Was this what you were looking for?
index.ndx   

thank you,
chinnu



--
View this message in context: 
http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010738.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re: error with g_dist

[Justin Lemkul]

On 8/26/13 4:39 PM, chinnu657 wrote:

I'm basically trying to see how the distance between the ligand and protein
changes with time using their centres of mass and the only way I've come
across is by using g_dist.

I'm pasting the contents from the terminal after the doing a gmxcheck on the
md_0_1.xtc file which is my .xtc file from the production simulation.

Checking file md_0_1.xtc
Reading frame   0 time0.000
# Atoms  33037
Precision 0.001 (nm)
Last frame   1000 time 2000.000


Item#frames Timestep (ps)
Step  10012
Time  10012
Lambda   0
Coords10012
Velocities   0
Forces   0
Box   10012

can I attach the index.ndx file again? Was this what you were looking for?
index.ndx 



Better would be for you to actually tell us what groups you chose (actual screen 
output from the selection would be best), rather than leave us to scroll through 
and guess.  If md_0_1.xtc has the whole system (33037 atoms), in principle that 
error should not have occurred.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: error with g_dist

[chinnu657]

Oh, sorry sorry. I see what your asking. I asked for 2 groups. One being the
protein and one being the ligand (JZ4)

screenshot.png
  

sorry, you may have to zoom in. I'm not sure how to snip on linux still. 
Chinnu



--
View this message in context: 
http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010740.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re: error with g_dist

[Justin Lemkul]

On 8/26/13 4:58 PM, chinnu657 wrote:

Oh, sorry sorry. I see what your asking. I asked for 2 groups. One being the
protein and one being the ligand (JZ4)

screenshot.png


sorry, you may have to zoom in. I'm not sure how to snip on linux still.


Copying and pasting text works well.  I understand what the list of groups is, 
but what groups *exactly* did you choose?


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: error with g_dist

[chinnu657]

1 and 13

Chinnu



--
View this message in context: 
http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010742.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re: error with g_dist

[Justin Lemkul]

On 8/26/13 5:05 PM, chinnu657 wrote:

1 and 13



I don't see how this error would be possible unless you accidentally chose group 
22.  Choosing 1 and 13 should be perfectly viable.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: error with g_dist

[chinnu657]

No, I chose 1 and 13. I just tried again, but the error is still the same..

Chinnu



--
View this message in context: 
http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010744.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re: error with g_dist

[Justin Lemkul]

On 8/26/13 5:35 PM, chinnu657 wrote:

No, I chose 1 and 13. I just tried again, but the error is still the same..



Send me your .tpr file, a coordinate file (.pdb or .gro) of the system, and your 
index file off-list and I will look into it.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: error with g_dist

[chinnu657]

I've copy, pasted the text after selection:

eading file md_0_1.tpr, VERSION 4.5.5 (single precision)
Group 0 ( System) has 33037 elements
Group 1 (Protein) has  1693 elements
Group 2 (  Protein-H) has  1301 elements
Group 3 (C-alpha) has   163 elements
Group 4 (   Backbone) has   489 elements
Group 5 (  MainChain) has   653 elements
Group 6 (   MainChain+Cb) has   805 elements
Group 7 (MainChain+H) has   815 elements
Group 8 (  SideChain) has   878 elements
Group 9 (SideChain-H) has   648 elements
Group10 (Prot-Masses) has  1693 elements
Group11 (non-Protein) has 31344 elements
Group12 (  Other) has15 elements
Group13 (JZ4) has15 elements
Group14 ( CL) has 6 elements
Group15 (  Water) has 31323 elements
Group16 (SOL) has 31323 elements
Group17 (  non-Water) has  1714 elements
Group18 (Ion) has 6 elements
Group19 (JZ4) has15 elements
Group20 ( CL) has 6 elements
Group21 ( Water_and_ions) has 31329 elements
Group22 (Protein_JZ4) has  1708 elements
Select a group: 1 13
Selected 1: 'Protein'
Select a group: Selected 13: 'JZ4'
Reading frame   0 time0.000   




--
View this message in context: 
http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010745.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: error with g_dist

[chinnu657]

md_0_1.tpr    -
production simulation .tpr file
3HTB_clean.pdb
   - .pdb
file after removing hz4 coordinates
JZ4.pdb    - jz4
coordinates
md_0_1.gro   
-production simulation .gro file
index.ndx    -
index file

Chinnu



--
View this message in context: 
http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010747.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re: error with g_dist

[Justin Lemkul]

On 8/26/13 5:47 PM, chinnu657 wrote:

md_0_1.tpr    -
production simulation .tpr file
3HTB_clean.pdb
   - .pdb
file after removing hz4 coordinates
JZ4.pdb    - jz4
coordinates
md_0_1.gro 
-production simulation .gro file
index.ndx    -
index file



The command:

echo 1 13 | g_dist -s md_0_1.tpr -f md_0_1.gro -n index.ndx

works perfectly fine for me with 4.5.5.  Try it and see what your outcome is.

-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: error with g_dist

[chinnu657]

Mine still gives me the same error. I don't quite understand why since it's
giving u the right output. Im using the same version as you too.

If you do not mind, could you give me the .xvg file? So that I can use it as
a result. Simultaneously, I'll see what I can do to solve the problem with
your help?

Chinnu



--
View this message in context: 
http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010749.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re: error with g_dist

[Justin Lemkul]

On 8/26/13 6:03 PM, chinnu657 wrote:

Mine still gives me the same error. I don't quite understand why since it's
giving u the right output. Im using the same version as you too.



My guess would be that your installation is buggy, usually the fault of a 
bad/outdated compiler.  Without significantly more detail about how your 
software was compiled and installed, it's simply conjecture, but a probable 
cause.  You could also try installing version 4.6.3, but I doubt the problem 
lies in Gromacs and rather the compilers, libraries, etc. available on your system.



If you do not mind, could you give me the .xvg file? So that I can use it as
a result. Simultaneously, I'll see what I can do to solve the problem with
your help?



I would be far more concerned with the fact that your Gromacs installation 
produces spurious error messages - who knows what else might be wrong?  Me 
providing you with a single number, which is not necessarily representative of 
any ensemble, does you no good.  I'm also not comfortable with providing someone 
with a data file so they can use it for a "submission" (as you called it 
earlier), which seems to imply some sort of assignment, given that it appears 
you are working through one of my tutorials.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: error with g_dist

[chinnu657]

ok that's ok then. this was the school system. so I can't really reinstall
it. I'll try and use a cluster. Hopefully, it works.

thanks a lot

Chinnu



--
View this message in context: 
http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010751.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

[gmx-users] Re: error with g_dist

[chinnu657]

I won't be submitting these though. just letting you know. I just need to
explain how all of these can be achieved. Just clarifying.

But thank you for all the help you've provided. It's been very valuable
help.

Chinnu



--
View this message in context: 
http://gromacs.5086.x6.nabble.com/error-with-g-dist-tp5010736p5010752.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

RE: [gmx-users] Coordination number

[Dallas Warren]

I don't know how g_rdf script uses any density to calculate the cumulative 
number RDF, I have always calculated the RDF then done the integration myself 
to determine the coordination number.

You need to look at the data you have in front of you, work out the density 
yourself, integrate yourself etc to understand and see what is actually 
happening.  That would be much faster than asking here on the emailing list.

Catch ya,

Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3 9903 9304
-
When the only tool you own is a hammer, every problem begins to resemble a 
nail. 

> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of Venkat Reddy
> Sent: Monday, 26 August 2013 10:02 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Coordination number
> 
> Sir
> 
> Thank you for the reply. The higher graph is also broader and I thought
> should then give a higher coordination number. Does gromacs use the box
> density? does it not use 4*pi*r2*g(r) for calculating rdf (thats what I
> read in a paper where the authors have used gromacs for simulation and
> analyses)?where is the density coming then?
> 
> Thank you
> 
> 
> On Wed, Aug 21, 2013 at 4:20 AM, Dallas Warren
> wrote:
> 
> > Peak can be higher, but if it is narrower the total area can still be
> > less.  Remember it is an area under the curve.  Additionally, that
> overall
> > system / box density that you are using may be different too, so that
> will
> > make a difference.
> >
> > Catch ya,
> >
> > Dr. Dallas Warren
> > Drug Discovery Biology
> > Monash Institute of Pharmaceutical Sciences, Monash University
> > 381 Royal Parade, Parkville VIC 3052
> > dallas.war...@monash.edu
> > +61 3 9903 9304
> > -
> > When the only tool you own is a hammer, every problem begins to
> resemble a
> > nail.
> >
> > > -Original Message-
> > > From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> > > boun...@gromacs.org] On Behalf Of Venkat Reddy
> > > Sent: Monday, 19 August 2013 8:11 PM
> > > To: Discussion list for GROMACS users
> > > Subject: [gmx-users] Coordination number
> > >
> > > Dear Gromacs Users,
> > >
> > > I have a query about the g_rdf utility. I have two different
> systems of
> > > water with Ionic Liquid 1 and Ionic Liquid 2. When I plot the rdf
> using
> > >
> > > g_rdf -f x_gro.pdb -s x.pdb -n rdf.ndx -o rdf1.xvg/rdf2.xvg -cn
> > > rdf1_cn.xvg/rdf2_cn.xvg -rdf res_com
> > >
> > > where rdf1/rdf2 is for water distribution around Ionic liquid 1/2,
> > >
> > > the rdf1.xvg clearly shows a higher first peak g(r) than the
> rdf2.xvg.
> > > Both
> > > also have minima at the same distance. However, the coordination
> number
> > > at
> > > first minima from rdf1_cn.xvg is lesser than the same from
> rd2_cn.xvg.
> > > How
> > > is this possible? If the peak is larger, the integration of it
> should
> > > give
> > > a higher value right?
> > >
> > > Please help.
> > >
> > >
> > > --
> > > With Best Wishes
> > > Venkat Reddy Chirasani
> > > PhD student
> > > Laboratory of Computational Biophysics
> > > Department of Biotechnology
> > > IIT Madras
> > > Chennai
> > > INDIA-600036
> > > --
> > > gmx-users mailing listgmx-users@gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > > * Please don't post (un)subscribe requests to the list. Use the
> > > www interface or send it to gmx-users-requ...@gromacs.org.
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > --
> > gmx-users mailing listgmx-users@gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> 
> 
> 
> --
> With Best Wishes
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search b