Re: [gmx-users] Regarding calculation of SDF

2018-05-31 Thread Mark Abraham 
Hi,

I can't tell whether you have a corrupted file, GROMACS has buggy code, or
the analysis procedure is wrong.

Mark

On Mon, May 28, 2018 at 4:18 AM Dilip.H.N  wrote:

> Hi,
> I want to calculate the Spatial Distribution Function of say N-terminal
> nitrogen atom and all the oxygen atoms of the water molecules.
> So, i have created the index file in which i have the nitrogen atom and all
> the oxygen atoms of water molecules. And here are my commands that i gave
> inorder to calculate SDF:
> gmx trjconv -s nptmd.tpr -f nptmd.xtc -n ndx_NOw.ndx -o abc.tng -ur compact
> -pbc whole
> gmx trjconv -s nptmd.tpr -f abc.tng -n ndx_NOw.ndx -o def.tng -fit
> rot+trans
> gmx spatial -s nptmd.tpr -n ndx_NOw.ndx -f def.tng -nab 10
>
> I get the following:
> Reading file nptmd.tpr, VERSION 2016.2 (single precision)
> Select group to generate SDF:
> Group 0 ( N) has 1 elements
> Group 1 ( OW) has   511 elements
> Select a group: 0
> Selected 0: 'N'
> Select group to output coords (e.g. solute):
> Group 0 ( N) has 1 elements
> Group 1 ( OW) has   511 elements
> Select a group: 1
> Selected 1: 'OW'
> TNG library: Cannot uncompress data block.
> /home/dilip/Downloads/gromacs-2016.2/src/external/tng_io/src/lib/tng_io.c:
> 5298
> TNG library: Cannot uncompress data block.
> /home/dilip/Downloads/gromacs-2016.2/src/external/tng_io/src/lib/tng_io.c:
> 5298
> Last frame  6 time 3.000
> Back Off! I just backed up grid.cube to ./#grid.cube.1#
> Counts per frame in all 27 cubes divided by 3.703704e-02
> Normalized data: average 1.00e+00, min 0.00e+00, max 2.70e+01
>
>
> and if i view the grid.cube file in vmd, i am unable to get a proper SDF/it
> is wired when i give an isovalues and change its values...
>
> How can i solve this..??
> Any suggestions are highly appreciated.
>
> Thank you.
>
> ---
> With Best Regards,
>
> Dilip.H.N
> PhD Student.
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Re: [gmx-users] Regarding calculation of SDF

2018-05-30 Thread Dilip.H.N 
Hello,
Hoping for a positive response...

Thank you.



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05/31/18,
9:26:54 AM

---
With Best Regards,

Dilip.H.N
PhD Student.

On Mon, May 28, 2018 at 7:47 AM, Dilip.H.N 
wrote:

> Hi,
> I want to calculate the Spatial Distribution Function of say N-terminal
> nitrogen atom and all the oxygen atoms of the water molecules.
> So, i have created the index file in which i have the nitrogen atom and
> all the oxygen atoms of water molecules. And here are my commands that i
> gave inorder to calculate SDF:
> gmx trjconv -s nptmd.tpr -f nptmd.xtc -n ndx_NOw.ndx -o abc.tng -ur
> compact -pbc whole
> gmx trjconv -s nptmd.tpr -f abc.tng -n ndx_NOw.ndx -o def.tng -fit
> rot+trans
> gmx spatial -s nptmd.tpr -n ndx_NOw.ndx -f def.tng -nab 10
>
> I get the following:
> Reading file nptmd.tpr, VERSION 2016.2 (single precision)
> Select group to generate SDF:
> Group 0 ( N) has 1 elements
> Group 1 ( OW) has   511 elements
> Select a group: 0
> Selected 0: 'N'
> Select group to output coords (e.g. solute):
> Group 0 ( N) has 1 elements
> Group 1 ( OW) has   511 elements
> Select a group: 1
> Selected 1: 'OW'
> TNG library: Cannot uncompress data block. /home/dilip/Downloads/gromacs-
> 2016.2/src/external/tng_io/src/lib/tng_io.c: 5298
> TNG library: Cannot uncompress data block. /home/dilip/Downloads/gromacs-
> 2016.2/src/external/tng_io/src/lib/tng_io.c: 5298
> Last frame  6 time 3.000
> Back Off! I just backed up grid.cube to ./#grid.cube.1#
> Counts per frame in all 27 cubes divided by 3.703704e-02
> Normalized data: average 1.00e+00, min 0.00e+00, max 2.70e+01
>
>
> and if i view the grid.cube file in vmd, i am unable to get a proper
> SDF/it is wired when i give an isovalues and change its values...
>
> How can i solve this..??
> Any suggestions are highly appreciated.
>
> Thank you.
>
> ---
> With Best Regards,
>
> Dilip.H.N
> PhD Student.
> [image: Mailtrack]
> 
>  Sender
> notified by
> Mailtrack
> 
>  05/28/18,
> 7:47:09 AM
>
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Re: [gmx-users] Regarding calculation of SDF

2018-05-28 Thread Dallas Warren 
What exactly is the issue?  It isn't clear what the problem is; the
fact it is having trouble with using the tng file format, or the
output in the cube file that is then loaded into vmd?
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 28 May 2018 at 12:17, Dilip.H.N  wrote:
> Hi,
> I want to calculate the Spatial Distribution Function of say N-terminal
> nitrogen atom and all the oxygen atoms of the water molecules.
> So, i have created the index file in which i have the nitrogen atom and all
> the oxygen atoms of water molecules. And here are my commands that i gave
> inorder to calculate SDF:
> gmx trjconv -s nptmd.tpr -f nptmd.xtc -n ndx_NOw.ndx -o abc.tng -ur compact
> -pbc whole
> gmx trjconv -s nptmd.tpr -f abc.tng -n ndx_NOw.ndx -o def.tng -fit rot+trans
> gmx spatial -s nptmd.tpr -n ndx_NOw.ndx -f def.tng -nab 10
>
> I get the following:
> Reading file nptmd.tpr, VERSION 2016.2 (single precision)
> Select group to generate SDF:
> Group 0 ( N) has 1 elements
> Group 1 ( OW) has   511 elements
> Select a group: 0
> Selected 0: 'N'
> Select group to output coords (e.g. solute):
> Group 0 ( N) has 1 elements
> Group 1 ( OW) has   511 elements
> Select a group: 1
> Selected 1: 'OW'
> TNG library: Cannot uncompress data block.
> /home/dilip/Downloads/gromacs-2016.2/src/external/tng_io/src/lib/tng_io.c:
> 5298
> TNG library: Cannot uncompress data block.
> /home/dilip/Downloads/gromacs-2016.2/src/external/tng_io/src/lib/tng_io.c:
> 5298
> Last frame  6 time 3.000
> Back Off! I just backed up grid.cube to ./#grid.cube.1#
> Counts per frame in all 27 cubes divided by 3.703704e-02
> Normalized data: average 1.00e+00, min 0.00e+00, max 2.70e+01
>
>
> and if i view the grid.cube file in vmd, i am unable to get a proper SDF/it
> is wired when i give an isovalues and change its values...
>
> How can i solve this..??
> Any suggestions are highly appreciated.
>
> Thank you.
>
> ---
> With Best Regards,
>
> Dilip.H.N
> PhD Student.
> [image: Mailtrack]
> 
> Sender
> notified by
> Mailtrack
> 
> 05/28/18,
> 7:47:09 AM
> --
> Gromacs Users mailing list
>
> * Please search the archive at 
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>
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>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
> mail to gmx-users-requ...@gromacs.org.
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[gmx-users] Regarding calculation of SDF

2018-05-27 Thread Dilip.H.N 
Hi,
I want to calculate the Spatial Distribution Function of say N-terminal
nitrogen atom and all the oxygen atoms of the water molecules.
So, i have created the index file in which i have the nitrogen atom and all
the oxygen atoms of water molecules. And here are my commands that i gave
inorder to calculate SDF:
gmx trjconv -s nptmd.tpr -f nptmd.xtc -n ndx_NOw.ndx -o abc.tng -ur compact
-pbc whole
gmx trjconv -s nptmd.tpr -f abc.tng -n ndx_NOw.ndx -o def.tng -fit rot+trans
gmx spatial -s nptmd.tpr -n ndx_NOw.ndx -f def.tng -nab 10

I get the following:
Reading file nptmd.tpr, VERSION 2016.2 (single precision)
Select group to generate SDF:
Group 0 ( N) has 1 elements
Group 1 ( OW) has   511 elements
Select a group: 0
Selected 0: 'N'
Select group to output coords (e.g. solute):
Group 0 ( N) has 1 elements
Group 1 ( OW) has   511 elements
Select a group: 1
Selected 1: 'OW'
TNG library: Cannot uncompress data block.
/home/dilip/Downloads/gromacs-2016.2/src/external/tng_io/src/lib/tng_io.c:
5298
TNG library: Cannot uncompress data block.
/home/dilip/Downloads/gromacs-2016.2/src/external/tng_io/src/lib/tng_io.c:
5298
Last frame  6 time 3.000
Back Off! I just backed up grid.cube to ./#grid.cube.1#
Counts per frame in all 27 cubes divided by 3.703704e-02
Normalized data: average 1.00e+00, min 0.00e+00, max 2.70e+01


and if i view the grid.cube file in vmd, i am unable to get a proper SDF/it
is wired when i give an isovalues and change its values...

How can i solve this..??
Any suggestions are highly appreciated.

Thank you.

---
With Best Regards,

Dilip.H.N
PhD Student.
[image: Mailtrack]

Sender
notified by
Mailtrack

05/28/18,
7:47:09 AM
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