Re: [gmx-users] Writing initial coordinates to trajectory files
From: Brian Helfrich <[EMAIL PROTECTED]>
Reply-To: [EMAIL PROTECTED],Discussion list for GROMACS users
To: Discussion list for GROMACS users
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 N1 2.105 0.744 2.070
1LYSHH12 2.056 0.668 2.027
1LYSHH23 2.190 0.761 2.021
full.trr:
natoms= 9035 step= 0 time=0.000e+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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Re: [gmx-users] Writing initial coordinates to trajectory files
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 N1 2.105 0.744 2.070
1LYSHH12 2.056 0.668 2.027
1LYSHH23 2.190 0.761 2.021
full.trr:
natoms= 9035 step= 0 time=0.000e+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
___
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RE: [gmx-users] Writing initial coordinates to trajectory files
I don't understand what it is you want. 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. But the initial coordinates are the ones you used to generate the tpr file, so I don't see why you would want those. editconf -f topol.tpr would also give you those coordinates in gro or pdb format. Berk. From: Brian Helfrich <[EMAIL PROTECTED]> Reply-To: [EMAIL PROTECTED],Discussion list for GROMACS users To: gmx-users@gromacs.org Subject: [gmx-users] Writing initial coordinates to trajectory files Date: Fri, 30 Nov 2007 10:43:28 -0500 Hello, Is there a setting, or some standard way to write out the initial coordinates of a system to the trajectory file instead of it waiting nstxout steps? Thanks very much, --Brian. PS. I sent this a couple days ago originally - must have gotten lost. Apologies if both make it through. -- Brian Helfrich www.nanorex.com ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _ Live Search, for accurate results! http://www.live.nl ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
