From: Brian Helfrich <[EMAIL PROTECTED]>
Reply-To: [EMAIL PROTECTED],Discussion list for GROMACS users
<gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@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
slightly:
after_em.gro:
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
full.trr:
natoms= 9035 step= 0 time=0.0000000e+00 lambda=
0
...
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.
--
Brian Helfrich
www.nanorex.com
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.
Berk.
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