[gmx-users] output unimaged trajectory?

david.evans at ulsop.ac.uk david.evans at ulsop.ac.uk
Wed Jul 14 10:18:42 CEST 2004

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


>> Is it possible to get mdrun to output a trajectory where
>> 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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