[gmx-users] -b option for g_order

[David van der Spoel]

Beate Griepernau wrote:
> The trajectory has a frame at 46000ps.
> The headers of the xtc-file are:
> [...
>    natoms=     21548  step=  22940000  time=     45880  prec=      1000
>    natoms=     21548  step=  22945000  time=     45890  prec=      1000
>    natoms=     21548  step=  22950000  time=     45900  prec=      1000
>    natoms=     21548  step=  22955000  time=     45910  prec=      1000
>    natoms=     21548  step=  22960000  time=     45920  prec=      1000
>    natoms=     21548  step=  22965000  time=     45930  prec=      1000
>    natoms=     21548  step=  22970000  time=     45940  prec=      1000
>    natoms=     21548  step=  22975000  time=     45950  prec=      1000
>    natoms=     21548  step=  22980000  time=     45960  prec=      1000
>    natoms=     21548  step=  22985000  time=     45970  prec=      1000
>    natoms=     21548  step=  22990000  time=     45980  prec=      1000
>    natoms=     21548  step=  22995000  time=     45990  prec=      1000
>    natoms=     21548  step=  23000000  time=     46000  prec=      1000
>    natoms=     21548  step=  23005000  time=     46010  prec=      1000
>    natoms=     21548  step=  23010000  time=     46020  prec=      1000
>    natoms=     21548  step=  23015000  time=     46030  prec=      1000
> ...]
> 
> The promblem seems to be resolved if we cut the large trajectory (0 to
> 50 ns) in smaller pieces, at least g_order works fine for a .xtc file
> including only frames from 45 to 48ns.

Is this the downsampled trajectory?
> 
> Beate
> 
> 
> 
> David van der Spoel wrote:
> 
> 
>>Beate Griepernau wrote:
>>
>>
>>>Dear all,
>>>
>>>I did a simulation of a membrane over a time period of 50ns writing out
>>>coordinates every picosecond.
>>>
>>>Next I edited the  .xtc-file to get a new .xtc file keeping only the
>>>data of every 10th step using trjconv and option -skip.
>>>
>>>On this new .xtc-file I applied g_order with different beginning and
>>>ending times (option -b and -e).
>>>
>>>For most beginning and ending times this procedure works well, but for
>>>beginning times around 46000ps the routine 'g_order' gets stuck:  I
>>>don't get an error message, but just the notice 'Skipping frame     
>>>0time 45890.000' .
>>>Using later start times > 46100 works well again.
>>>I checked my .xtc file using several other routines,  e.g. gmxcheck and
>>>trjconv to write a snapshot of the trajectory at the time im question,
>>>and it worked well.
>>>
>>>Does anybody know why this problem occurs and how it can be solved?
>>> 
>>>
>>
>>This is probably not specific for g_order. Does the trajectory have a
>>frame at 46000?
>>Could it be that the original framenumbers are still in place (i.e.
>>step etc.)?
>>Please run gmxdump on the xtc file and print the headers of the frames
>>at 46000 and the one before and after and send it to the list.
>>
>>
>>
>>>Thanks for your help.
>>>
>>>Regards,
>>>Beate
>>>_______________________________________________
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>>> 
>>>
>>
>>
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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