[gmx-users] Trajectory files are too big

Bjoern Windshuegel bjorn.windshugel at uku.fi
Tue Jan 22 07:24:58 CET 2008


you can easily restrict the amount of data if you set the frequency of writing 
out coordinates accordingly. Check the manual page 138 (7.3.7, output 
control). The standard settings (100) are quite small, I recommend to use at 
least 1000 for writing out coordinates. So the amount of data should be 
reduced significantly. 

Best regards,


> Dear Gromacs Users,
> After a long time I am working with gromacs. Though at the starting I got
> some problem in installation with the rpm, (a conflict error with mono-web)
> I installed it anyway forcefully. Problem is the trajectory files that I am
> getting are too big. I have run a mdrun for 2ns on a protein+water system
> consisting of 60149 atoms in 18875 residues (as after running 'genbox'
> using spc216.gro). The .xtc, and .trr files I am getting are of 19GB and
> 12GB respectively. Is this normal, or I have some  problem with my gromacs?
> My hard disk space is 80GB. I am just worrying about what should I do if I
> will have to run it for 4ns or more than that?? If these files are so big
> how many MD will I be able to run? Is double precision installation of
> gromacs helpful? will I get these trajectory files in some compressed
> format??
> Please help.
> Nabajyoti Goswami
> Ph.D Student.
> Center for Biotechnology,
> Anna University,
> Chennai-600025
> Tamil Nadu.
> Mobile: 09840487093

Dr. Björn Windshügel

Department of Pharmaceutical Chemistry
University of Kuopio
P.O. Box 1627
70211 Kuopio, FINLAND

Email: bjorn.windshugel at uku.fi
Phone: (+358) 17 162463
Fax:   (+358) 17 162456
Web:   www.uku.fi/farmasia/fake/modelling/index.shtml

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