[gmx-users] can the GROMACS transform the amber trajectory to GROMACS
Nguyen Hoang Phuong
phuong at theochem.uni-frankfurt.de
Tue May 28 12:50:24 CEST 2002
I think this forwarded email can help you.
---------- Forwarded message ----------
Date: Fri, 17 May 2002 21:57:07 +0200 (CEST)
From: David van der Spoel <spoel at xray.bmc.uu.se>
Cc: gmx-users at gromacs.org
Subject: Re: [gmx-users] Trajectory analysis tools.
On Fri, 17 May 2002, A.Madhumalar wrote:
> I am new user to this package. i wanted to use the MD trajectory analysis tool in
>this software for calculating covariance.The thing is i am having trajectories
>generated form AMBER package.can anyone tell me how to start off with
>gromacs trajectory tools? Thanks for any help.
Yes, as long as they are ascii.
rename them to .g87 files (these are the same as amber trajs)
and then you have to know the number of atoms, the timestep and whether
there is a box in the file.
you can also convert your traj. to .xtc to save space
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Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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