[gmx-users] trajectory file

[Alexey Shvetsov]

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