Paymon Pirzadeh wrote:
Hi Tom,
Thanks for the tip. It worked on the command line and I had 3000 frames.
But when I fed the file to VMD, it showed only 1800 frames!? Although
the initial and final configurations looked correct. I still am not sure
what possibly goes wrong!?
VMD is not an appropriate method for determining the contents of a file. VMD
can only load as many frames as memory will allow. Run gmxcheck on all of your
.xtc files to determine how many frames are present, what the starting times
are, etc.
-Justin
Payman
On Mon, 2009-11-02 at 10:50 +0000, TJ Piggot wrote:
You should use the -settime option, I think it should solve your problem.
Tom
--On Monday, November 02, 2009 00:21:31 -0800 Payman Pirzadeh
<ppirz...@ucalgary.ca> wrote:
Your second guess is correct! I used grompp to restart (I had thought it
might provide me with the chance to change things if needed). I was
surprised initially when "cat" command did not work! The number of frames
were most of the time less than what it should be.
I also checked the 'trjcat -h'. I did not specifically understand how I
might be able to get over this issue. Any advices?
Payman
-----Original Message-----
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Mark Abraham
Sent: Sunday, November 01, 2009 8:37 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] trjcat xtc files
Paymon Pirzadeh wrote:
Sorry,
My command line was:
trjcat_d_mpi -f AFPI_Ih1010_54_58_Npt265_2.xtc
AFPI_Ih1010_54_58_Npt265_3.xtc AFPI_Ih1010_54_58_Npt265_4.xtc
AFPI_Ih1010_54_58_Npt265_5.xtc AFPI_Ih1010_54_58_Npt265_6.xtc -o
AFPI_Ih1010_54_58_Npt265_merged2-6.xtc
the "_d_mpi" is the suffix used for double precision and parallel
version of the installed gromacs.
OK so now we have some idea what you might be trying to do. The most
likely causes are that the first few trajectories have no frames, or
that each frame in the earlier trajectories is common to one in the last
trajectory. This might happen if you were using grompp to do restarts,
or have previously assigned duplicate times somehow. If so, find a
better workflow in future. Consult trjcat -h for clues on how to get
around this.
Mark
Payman
On Mon, 2009-11-02 at 15:08 +1100, Mark Abraham wrote:
Paymon Pirzadeh wrote:
Hello,
I am trying to concatenate several xtc files. When I use the trjcat, it
only writes the last file into the output file! where the problem could
be?
In your command line. Why didn't you tell us what it was? :-)
Mark
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----------------------
TJ Piggot
t.pig...@bristol.ac.uk
University of Bristol, UK.
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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