[gmx-users] [Fwd: Question about CHARMM trj to GROMACS trj]

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 28 16:56:37 CEST 2007

Mark Abraham wrote:

Please keep these discussions on the list. Not only am I not a personal 
free help service, but everyone benefits from the on-line archives, and 
other may benefit from any answer you receive.

I don't know precisely what you mean by "Is there any way we can do 
that? How can I analyze 10-20ns trajectories using pdb files?" You can 
pretend that multiple structures in one PDB file are a simulation 
trajectory, and gromacs tools will read and write a variety of 
trajectory formats according to the filename suffix you give to the tool 
you're invoking. See "man trjconv" among others. It does sound like you 
should do some more homework, like reading relevant sections of the 
gromacs manual and doing some tutorial exercises.


> -------- Original Message --------
> Subject: Question about CHARMM trj to GROMACS trj
> Date: Wed, 28 Mar 2007 10:07:32 -0400
> From: Hwankyu Lee <leehk at umich.edu>
> To: mark.abraham at anu.edu.au
> Dear Dr. Abraham,
> Thank you very much for your answer below. As you suggested, pdb file
> can be compatible, but it will be better to have .xtc files in order to
> analyze trajectories with enough sampling (10~20ns). Is there any way
> we can do that? How can I analyze 10-20ns trajectories using pdb files?
> Thanks,
> best,
> Hwankyu.
> On Mar 27, 2007, at 3:06 PM, gmx-users-request at gromacs.org wrote:
> Message: 4
> Date: Wed, 28 Mar 2007 01:26:07 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Converting CHARMM trajectories (.trj) to
>     GROMACS    trajectories (.xtc)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4609378F.2050505 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> Hwankyu Lee wrote:
> Dear gmx-users,
> I would like to analyze CHARMM trajectories in GROMACS, and wonder if
> there are available scripts or tools to convert CHARMM traj to GROMACS
> traj (.xtc).  I've searched the contributed software and forum
> sections, and it looks like there is a script for that, but couldn't
> find it.  If you can provide me scripts for that, it'll be appreciated.
> I'm not aware of one... if it looks like there is a script for it, why
> couldn't you find it? :-)
> I think you should explore finding an intermediate format, like PDB,
> through which you can convert one to the other - you will lose
> precision, but that will not matter for analysis.
> Mark
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