[gmx-users] splitting a trajectory

Discussion:

Ramachandran G

2009-12-11 04:05:02 UTC

Dear gromacs users:
Can any one tell me how can i split a trajectory file from a
specific time interval of my interest.
For example if i have a trajectory file up to 0-100ps, and my interest is to
consider part of the trajectory from 50-75ps,
how i can go about it either by splitting the trajectory file. Thanks for
your help

Rama
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Justin A. Lemkul

2009-12-11 04:08:00 UTC

Permalink

Post by Ramachandran G
Can any one tell me how can i split a trajectory file from a
specific time interval of my interest.
For example if i have a trajectory file up to 0-100ps, and my interest
is to consider part of the trajectory from 50-75ps,
how i can go about it either by splitting the trajectory file. Thanks
for your help

Make use of the -b and -e flags, which should be present in all of the analysis
tools.

-Justin

Post by Ramachandran G
Rama

Dallas B. Warren

2009-12-11 04:45:21 UTC

Permalink

Another option is to create a new trajectory file to use in your analysis, using trjconv

Catch ya,

Dr Dallas Warren
Pharmacy and Pharmaceutical Sciences
Monash University

A polar bear is a Cartesian bear that has undergone a polar transformation

-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of Justin A. Lemkul
Sent: Fri 12/11/2009 3:08 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] splitting a trajectory

Make use of the -b and -e flags, which should be present in all of the analysis
tools.

-Justin

Post by Ramachandran G
Rama

--
========================================

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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Ramachandran G

2009-12-11 05:05:51 UTC

Permalink

Thanks for your help.
I have tried the command

trjconv -f traj.trr -s AFP-500ps.tpr -b 87001 -e 99000 -o test.gro

but nothing was written on output file(test.gro) and got the message

"WARNING no output, trajectory ended at 500"

Am i doing it right?

Post by Justin A. Lemkul

Post by Ramachandran G
Can any one tell me how can i split a trajectory file from a
specific time interval of my interest.
For example if i have a trajectory file up to 0-100ps, and my interest is
to consider part of the trajectory from 50-75ps,
how i can go about it either by splitting the trajectory file. Thanks for
your help

Make use of the -b and -e flags, which should be present in all of the
analysis tools.
-Justin
Rama
--
========================================
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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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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--
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.
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Justin A. Lemkul

2009-12-11 05:13:11 UTC

Permalink

Post by Ramachandran G
Thanks for your help.
I have tried the command
trjconv -f traj.trr -s AFP-500ps.tpr -b 87001 -e 99000 -o test.gro
but nothing was written on output file(test.gro) and got the message
"WARNING no output, trajectory ended at 500"
Am i doing it right?

Ramachandran G

2009-12-11 09:51:24 UTC

Permalink

Thanks, it works when i give proper time.

Previously i made mistake by giving the time frame number.
Rama

Post by Justin A. Lemkul

Obviously not. If your trajectory ended at 500 ps, then frames at 87001
and 99000 ps clearly don't exist.
-Justin
--
========================================
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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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-request at gromacs.org.
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