Re: [gmx-users] extracting specfic trajectories?

[Justin A. Lemkul]

minnale wrote:
 
Thanks Justin for your prompt response,

I have issued the command
trjconv -f 5ns_trj.xtc -skip 1000 -o every1000steps.xtc, means the 
output trajectory will contain only 1000th step interval values till 
5ns, excluding remaining. How can I know that whether generated 
trajectory file right or wrong? 


The value passed to -skip is the number of frames to skip, not necessarily the 
time interval or number of steps that are skipped.


You can check the resulting trajectory with gmxcheck.

-Justin


Thanks alot for any suggestion.
On Sat, 13 Sep 2008 Justin A.Lemkul wrote :
 >
 >
 >minnale wrote:
 >>  Hi all,
 >>I have run the simulation with 100 steps interval in .log file till 
5ns, now I want to extract the new trajectory file should conatin with 
1000 steps inerval trajectories excluding remain steps. I want new 
trajectory like 1000, 2000, 3000, 4000, 5000,... steps.

 >>Could anyone tell me detail suggestion please.
 >>Thanks in advance.
 >>
 >
 >Trajectory manipulations are done with trjconv.  Have a look at 
trjconv -skip.

 >
 >-Justin
 >
 >>
 >>
 >>Ebay 


 >>
 >>
 >>
 >>
 >>___
 >>gmx-users mailing listgmx-users@gromacs.org
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posting!
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 >-- 
 >
 >Justin A. Lemkul
 >Graduate Research Assistant
 >Department of Biochemistry
 >Virginia Tech
 >Blacksburg, VA
 >jalemkul[at]vt.edu | (540) 231-9080
 >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
 >
 >



Rediff Shopping 





--


Justin A. Lemkul
Graduate Research Assistant
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: Re: [gmx-users] extracting specfic trajectories?

[minnale]

  
Thanks Justin for your prompt response,
I have issued the command
trjconv -f 5ns_trj.xtc -skip 1000 -o every1000steps.xtc, means the output 
trajectory will contain only 1000th step interval values till 5ns, excluding 
remaining. How can I know that whether generated trajectory file right or 
wrong?   
Thanks alot for any suggestion.
On Sat, 13 Sep 2008 Justin A.Lemkul wrote :
>
>
>minnale wrote:
>>  Hi all,
>>I have run the simulation with 100 steps interval in .log file till 5ns, now 
>>I want to extract the new trajectory file should conatin with 1000 steps 
>>inerval trajectories excluding remain steps. I want new trajectory like 1000, 
>>2000, 3000, 4000, 5000,... steps.
>>Could anyone tell me detail suggestion please.
>>Thanks in advance.
>>
>
>Trajectory manipulations are done with trjconv.  Have a look at trjconv -skip.
>
>-Justin
>
>>
>>
>>Ebay 
>>> PROTECTED]/2401775_2394076/2397136/1?PARTNER=3&OAS_QUERY=null>
>>
>>
>>
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>>http://www.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 [EMAIL PROTECTED]
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>-- 
>
>Justin A. Lemkul
>Graduate Research Assistant
>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] pdb_to_xvzr not working

[Justin A. Lemkul]

Morteza Khabiri wrote:

Dear

I want make hole in my system. Because of this I oblige to use MSMS programm
to calculate the surface of my protein. Before using MSMS we should change
pdb file format to xyzr  file format. I should use pdb_to_xvzr to produce
xvzr file. Unfortunately I couldn't run  pdb_to_xvzr. After running i
faced with the following error:

./pdb_to_xyzr: line 102: nawk: command not found

thats very nice of you if someone could help me how to active pdb_to_xyzr.
I use chmod but it did not work.



"nawk" is a Unix/Linux utility.  It looks like the program requires this tool to 
work, so you need to install it.  If it is installed, you will need to add its 
location to your $PATH.


-Justin


Thanks alot

Morteza


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--


Justin A. Lemkul
Graduate Research Assistant
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] pdb_to_xvzr not working

[Morteza Khabiri]

Dear

I want make hole in my system. Because of this I oblige to use MSMS programm
to calculate the surface of my protein. Before using MSMS we should change
pdb file format to xyzr  file format. I should use pdb_to_xvzr to produce
xvzr file. Unfortunately I couldn't run  pdb_to_xvzr. After running i
faced with the following error:

./pdb_to_xyzr: line 102: nawk: command not found

thats very nice of you if someone could help me how to active pdb_to_xyzr.
I use chmod but it did not work.

Thanks alot

Morteza


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Re: [gmx-users] defining group

[Omer Markovitch]

Thank you both! Omer.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/


On Sat, Sep 13, 2008 at 15:57, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:

>
>
> Omer Markovitch wrote:
>
>> Hello,
>> I would like to ask for your help in defining groups:
>> Say I have a protein. I would like to have two groups (1) the Calpha
>> backbone (2) everything else.
>> Later on, I will want to freeze the Calpha group.
>> How can I define these groups? Where?
>> I have looked in the manual, but I do not understand how to do it and in
>> which files.
>>
>
> Groups are defined in index files (.ndx), which are created with make_ndx.
> Calpha is a default group read in from a protein structure.  To create a
> group that is everything but Calpha (group 3 in the make_ndx list), you
> would use
>
> !3
>
> at the make_ndx prompt.
>
> -Justin
>
>  Thank you, Omer Markovitch.
>>
>> Koby Levy research group,
>> Weizmann Institute of Science.
>> http://www.weizmann.ac.il/sb/faculty_pages/Levy/
>>
>>
>> 
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
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>> interface or send it to [EMAIL PROTECTED]
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>>
>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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
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Re: [gmx-users] defining group

[Justin A. Lemkul]

Omer Markovitch wrote:

Hello,
I would like to ask for your help in defining groups:
Say I have a protein. I would like to have two groups (1) the Calpha 
backbone (2) everything else.

Later on, I will want to freeze the Calpha group.
How can I define these groups? Where?
I have looked in the manual, but I do not understand how to do it and in 
which files.


Groups are defined in index files (.ndx), which are created with make_ndx. 
Calpha is a default group read in from a protein structure.  To create a group 
that is everything but Calpha (group 3 in the make_ndx list), you would use


!3

at the make_ndx prompt.

-Justin


Thank you, Omer Markovitch.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/




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--


Justin A. Lemkul
Graduate Research Assistant
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] defining group

[David van der Spoel]

Omer Markovitch wrote:

Hello,
I would like to ask for your help in defining groups:
Say I have a protein. I would like to have two groups (1) the Calpha 
backbone (2) everything else.

Later on, I will want to freeze the Calpha group.
How can I define these groups? Where?

Using make_ndx
backbone is predefined, e.g. group 4 and protein is usually 1
then you select
1 & !4

I have looked in the manual, but I do not understand how to do it and in 
which files.

Thank you, Omer Markovitch.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/




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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
[EMAIL PROTECTED]   [EMAIL PROTECTED]   http://folding.bmc.uu.se
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[gmx-users] defining group

[Omer Markovitch]

Hello,
I would like to ask for your help in defining groups:
Say I have a protein. I would like to have two groups (1) the Calpha
backbone (2) everything else.
Later on, I will want to freeze the Calpha group.
How can I define these groups? Where?
I have looked in the manual, but I do not understand how to do it and in
which files.
Thank you, Omer Markovitch.

Koby Levy research group,
Weizmann Institute of Science.
http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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Re: [gmx-users] extracting specfic trajectories?

[Justin A. Lemkul]

minnale wrote:
 
Hi all,
I have run the simulation with 100 steps interval in .log file till 5ns, 
now I want to extract the new trajectory file should conatin with 1000 
steps inerval trajectories excluding remain steps. I want new trajectory 
like 1000, 2000, 3000, 4000, 5000,... steps.

Could anyone tell me detail suggestion please.
Thanks in advance.



Trajectory manipulations are done with trjconv.  Have a look at trjconv -skip.

-Justin




Ebay 






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--


Justin A. Lemkul
Graduate Research Assistant
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] extracting specfic trajectories?

[minnale]

  
Hi all, 
I have run the simulation with 100 steps interval in .log file till 5ns, now I 
want to extract the new trajectory file should conatin with 1000 steps inerval 
trajectories excluding remain steps. I want new trajectory like 1000, 2000, 
3000, 4000, 5000,... steps.
Could anyone tell me detail suggestion please.
Thanks in advance.___
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