[gmx-users] trjcat xtc files

[XAvier Periole]

On Nov 2, 2009, at 18:13, Paymon Pirzadeh <ppirzade at ucalgary.ca> 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!
Memory limit?
>
> 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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>>>>>
>>>>
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>>
>>
>>
>> ----------------------
>> TJ Piggot
>> t.piggot at bristol.ac.uk
>> University of Bristol, UK.
>>
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>>
>
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