Re: [gmx-users] combine two gro into one

[Tom Piggot]

Or you can do the renumbering through feeding the file through editconf.

Tom

Justin A. Lemkul wrote:

Sikandar Mashayak wrote:
  
yeah I know its simple, but only concern I have is that, the index of 
atom/residue in two files may not be in agreement, so I have to 
change/shift index of atoms in one of the file.


but anyway I guess I will have to do it manually




That part can be done with genconf -renumber.

-Justin

  

thanks
sikandar

On Thu, May 13, 2010 at 10:02 PM, Justin A. Lemkul > wrote:




Sikandar Mashayak wrote:

I need to do water channel simulations... I have two gro files
with me...one for wall atoms and one for water atoms...assuming
the co-ordinates of atoms are appropriate, I just need to rename
the indices of each atom appropriately and append one file to
anotherI plan to do it by hand...but it will be great if
there is an automatic way of doing it in gromacs?


This is a simple task that can be done with the Unix 'cat' command.
 Thus there is no Gromacs tool that reproduces this function.  A few
seconds with a text editor after concatenation to remove unnecessary
title lines and box vectors and you're done, assuming (as you've
said) that all the coordinates are appropriately defined.  The whole
process probably takes less typing than sending this email :)

-Justin

thanks
sikandar


-- 



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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--
Dr Thomas Piggot
University of Southampton, UK.

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Re: [gmx-users] combine two gro into one

[Justin A. Lemkul]

Sikandar Mashayak wrote:
yeah I know its simple, but only concern I have is that, the index of 
atom/residue in two files may not be in agreement, so I have to 
change/shift index of atoms in one of the file.


but anyway I guess I will have to do it manually



That part can be done with genconf -renumber.

-Justin


thanks
sikandar

On Thu, May 13, 2010 at 10:02 PM, Justin A. Lemkul > wrote:




Sikandar Mashayak wrote:

I need to do water channel simulations... I have two gro files
with me...one for wall atoms and one for water atoms...assuming
the co-ordinates of atoms are appropriate, I just need to rename
the indices of each atom appropriately and append one file to
anotherI plan to do it by hand...but it will be great if
there is an automatic way of doing it in gromacs?


This is a simple task that can be done with the Unix 'cat' command.
 Thus there is no Gromacs tool that reproduces this function.  A few
seconds with a text editor after concatenation to remove unnecessary
title lines and box vectors and you're done, assuming (as you've
said) that all the coordinates are appropriately defined.  The whole
process probably takes less typing than sending this email :)

-Justin

thanks
sikandar


-- 



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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Please search the archive at http://www.gromacs.org/search before
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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] combine two gro into one

[Sikandar Mashayak]

yeah I know its simple, but only concern I have is that, the index of
atom/residue in two files may not be in agreement, so I have to change/shift
index of atoms in one of the file.

but anyway I guess I will have to do it manually

thanks
sikandar

On Thu, May 13, 2010 at 10:02 PM, Justin A. Lemkul  wrote:

>
>
> Sikandar Mashayak wrote:
>
>> I need to do water channel simulations... I have two gro files with
>> me...one for wall atoms and one for water atoms...assuming the co-ordinates
>> of atoms are appropriate, I just need to rename the indices of each atom
>> appropriately and append one file to anotherI plan to do it by
>> hand...but it will be great if there is an automatic way of doing it in
>> gromacs?
>>
>>
> This is a simple task that can be done with the Unix 'cat' command.  Thus
> there is no Gromacs tool that reproduces this function.  A few seconds with
> a text editor after concatenation to remove unnecessary title lines and box
> vectors and you're done, assuming (as you've said) that all the coordinates
> are appropriately defined.  The whole process probably takes less typing
> than sending this email :)
>
> -Justin
>
>  thanks
>> sikandar
>>
>>
> --
> 
>
> 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
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
>
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Re: [gmx-users] combine two gro into one

[Justin A. Lemkul]

Sikandar Mashayak wrote:
I need to do water channel simulations... I have two gro files with 
me...one for wall atoms and one for water atoms...assuming the 
co-ordinates of atoms are appropriate, I just need to rename the indices 
of each atom appropriately and append one file to anotherI plan to 
do it by hand...but it will be great if there is an automatic way of 
doing it in gromacs?




This is a simple task that can be done with the Unix 'cat' command.  Thus there 
is no Gromacs tool that reproduces this function.  A few seconds with a text 
editor after concatenation to remove unnecessary title lines and box vectors and 
you're done, assuming (as you've said) that all the coordinates are 
appropriately defined.  The whole process probably takes less typing than 
sending this email :)


-Justin


thanks
sikandar



--


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] combine two gro into one

[Sikandar Mashayak]

I need to do water channel simulations... I have two gro files with me...one
for wall atoms and one for water atoms...assuming the co-ordinates of atoms
are appropriate, I just need to rename the indices of each atom
appropriately and append one file to anotherI plan to do it by
hand...but it will be great if there is an automatic way of doing it in
gromacs?

thanks
sikandar
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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