[gmx-users] Writing initial coordinates to trajectory files

Berk Hess gmx3 at hotmail.com
Mon Dec 3 11:40:45 CET 2007

>From: Brian Helfrich <brian at nanorex.com>
>Reply-To: helfrich at nanorex.com,Discussion list for GROMACS users 
><gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] Writing initial coordinates to trajectory files
>Date: Fri, 30 Nov 2007 12:55:20 -0500
>Berk Hess wrote:
>>The initial coordinates are written immediately to the trr file,
>>although the file system might buffer data, you so could have to wait
>>until some more frames have been written.
>Thanks, I see that now. It seems that somewhere between grompp and mdrun's 
>initial trajectory output, my initial coordinates did change ever so 
>    1LYSH     N    1   2.105   0.744   2.070
>    1LYSH    H1    2   2.056   0.668   2.027
>    1LYSH    H2    3   2.190   0.761   2.021
>   natoms=      9035  step=         0  time=0.0000000e+00  lambda=         
>   ...
>      x[    0]={ 2.10518e+00,  7.43687e-01,  2.07004e+00}
>      x[    1]={ 2.05600e+00,  6.68002e-01,  2.02700e+00}
>      x[    2]={ 2.19043e+00,  7.61087e-01,  2.02075e+00}
>But step 0 coordinates are output as you said, thanks.
>Brian Helfrich

A gro file does not have full accuracy.
Probably mdrun changed the initial coordinates because of the constraints.
The rounded coordinates in the gro file do not obey the constraints exactly.


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