[gmx-users] trajectory file

Alexey Shvetsov alexxy at omrb.pnpi.spb.ru
Tue Dec 15 17:12:21 CET 2015

Timofey Tyugashev писал 15-12-2015 08:41:
> 04.12.2015 14:43, gromacs.org_gmx-users-request at maillist.sys.kth.se 
> пишет:
>> I ran the production MD and got the trajectory file (xtcformat) but as 
>> I?m new to MD I don?t know how to visualize it. I opened it withvmd 
>> and it could read the atoms and frames but didn?t show anything when 
>> playingthe frames. I don?t know whether another program can do it or 
>> my xtc is notcorrect.
> You can also read GROMACS trajectories with PyMOL. It offers quite
> nice visualisation options.
> Use 'load' command to load the coordinate file first, then load the
> trajectory itself using 'load_traj' command.

Only problem with pymol is that it eats very large amount of memory. I 
cannot evel load trajectory of large nucleoprotein complex (~200k atoms 
for complex itself without solvent) if it has ~1000 frames on 
workstation with 64G ram.

Best Regards,
Alexey 'Alexxy' Shvetsov, PhD
Department of Molecular and Radiation Biophysics
FSBI Petersburg Nuclear Physics Institute, NRC Kurchatov Institute,
Leningrad region, Gatchina, Russia
mailto:alexxyum at gmail.com
mailto:alexxy at omrb.pnpi.spb.ru

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