[gmx-users] output unimaged trajectory?

[david.evans at ulsop.ac.uk]

Thanks for the reply. I have been using  `trjconv -pbc nojump', but
the molecule then appears to translate through the system, in
contrast to the same system simulated in Amber. I want to know if
this is because of the imaging or whether there is a real physical
difference between the two MD engines. I've tried to make the input
parameters as compatible as possible, particularly the centre of mass
motion removal.

So, the main question was about mdrun, which seems to output imaged
trajectories by default. Could you confirm that it is impossible to
get mdrun to output unimaged coordinates?

Thank you

Dave

>> Is it possible to get mdrun to output a trajectory where
coordinates
>> are not wrapped into the periodic box?
>> I'm thinking of the default Amber behaviour (with IWRAP=0), if that
>> helps anyone understand what I mean. I'm looking for maximum
>> compatibility with Amber, 

>trjconv -pbc nojump
>
>> Thank you
>> 
>> Dave Evans
>> London School of Pharmacy
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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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