[gmx-users] can we analyse Gromacs trajectory with jupyter?

[Hai Nguyen]

On Fri, Jun 24, 2016 at 11:04 AM, Albert <mailmd2011 at gmail.com> wrote:

> Great to hear that. Hopefully it can support  .xtc format soon, since the
> .trr file is really huge.
>
>
Actually you can use mdtraj to read .xtc format and construct pytraj's
object in memory.
there is an tutorial here:
http://amber-md.github.io/pytraj/latest/tutorials/interface_with_mdtraj_.html

Hai


>
> On 06/24/2016 04:36 PM, Hai Nguyen wrote:
>
>> Hi,
>>
>> cpptraj is able to read TRR format too. cpptraj can read a pdb file as
>> Topology, so no need to do any conversion to " an equivalent AMBER
>> topology"
>> I hope that Dan Roe (cc) can find a time slot to implement xtc and  tng
>> parser soon.
>>
>> @Albert: meanwhile, you can absolutely use pytraj (python interface of
>> cpptraj)<https://github.com/Amber-MD/pytraj>  and NGLView
>> <https://github.com/arose/nglview>  for your gromacs data analysis and
>> visualization (need to convert to .trr format thought).
>>
>> cheers
>> Hai
>>
>>
>>
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