[gmx-users] trjcat xtc files

[Justin A. Lemkul]

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 
>> <ppirzade at 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-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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>>
>>
>> ----------------------
>> TJ Piggot
>> t.piggot at bristol.ac.uk
>> University of Bristol, UK.
>>
>> _______________________________________________
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>>
> 
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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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