[gmx-users] trajectory file
tyugashev at niboch.nsc.ru
Thu Dec 17 05:58:17 CET 2015
16.12.2015 00:55, gromacs.org_gmx-users-request at maillist.sys.kth.se пишет:
>> 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.
Personally I haven't noticed any qualitative difference in memory
consumption compared with vmd when viewing same .xtc files. It either
works or it does not. But my simulations are different (~5-10k atoms
without solvent and tens of ns on 32G RAM system).
IIRC, there were some options in pymol for processing trajectories.
Maybe they do influence the performance.
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