Re: [gmx-users] trjcat: joining randomized PDB files

[Justin Lemkul]

On 5/9/13 9:50 AM, Anirban wrote:


Thanks a lot Justin, for the reply.
But with -settime for every file I have to interactively give arbitrary values.
I have around 500 PDB files for one part of the trajectory and there are total
10 parts. So its very difficult to repeat this for around 5000 times. Is there
any other option. trjcat reads the randomized PDB files serially, so can't it
just concatenate the files in that order? Or am I missing something?



Interactive prompts like this are easy to use in scripts.

http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts

I have never tried with trjcat, but it seems to me that you can easily loop 
through any arbitrary set of numbers stored in a variable as the time value to 
be passed to trjcat.


-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] trjcat: joining randomized PDB files

[Anirban]

Thanks a lot Justin, for the reply.
But with -settime for every file I have to interactively give arbitrary
values. I have around 500 PDB files for one part of the trajectory and
there are total 10 parts. So its very difficult to repeat this for around
5000 times. Is there any other option. trjcat reads the randomized PDB
files serially, so can't it just concatenate the files in that order? Or am
I missing something?

Thanks again.

Regards,

Anirban

On Thu, May 9, 2013 at 7:07 PM, Justin Lemkul  wrote:

>
>
> On 5/9/13 9:35 AM, Anirban wrote:
>
>> Dear ALL,
>>
>> I want to randomize the frames of my trajectory for calculating
>> convergence. For this, I have dropped the frames as PDB files using
>> trjconv
>> and then renamed them randomly. Now I want to join these randomized PDB
>> frames to get a randomized trajectory using trajcat. But somehow trjcat
>> always joins them in proper frame order (inspite of completely random PDB
>> file names). How can I join the randomly to get a randomized trajectory?
>> Any suggestion is welcome.
>>
>>
> Use -settime and give them arbitrary time values.
>
> -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
>
> ==**==
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] trjcat: joining randomized PDB files

[Justin Lemkul]

On 5/9/13 9:35 AM, Anirban wrote:

Dear ALL,

I want to randomize the frames of my trajectory for calculating
convergence. For this, I have dropped the frames as PDB files using trjconv
and then renamed them randomly. Now I want to join these randomized PDB
frames to get a randomized trajectory using trajcat. But somehow trjcat
always joins them in proper frame order (inspite of completely random PDB
file names). How can I join the randomly to get a randomized trajectory?
Any suggestion is welcome.



Use -settime and give them arbitrary time values.

-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] trjcat: joining randomized PDB files

[Anirban]

Dear ALL,

I want to randomize the frames of my trajectory for calculating
convergence. For this, I have dropped the frames as PDB files using trjconv
and then renamed them randomly. Now I want to join these randomized PDB
frames to get a randomized trajectory using trajcat. But somehow trjcat
always joins them in proper frame order (inspite of completely random PDB
file names). How can I join the randomly to get a randomized trajectory?
Any suggestion is welcome.

Regards,

Anirban
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