[gmx-users] trjcat xtc files

[Payman Pirzadeh]

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-bounces at gromacs.org [mailto:gmx-users-bounces at 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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> 
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