[gmx-users] trajectory file
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
>> 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.
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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