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. _ Talk with your online friends with Messenger http://www.join.msn.com/messenger/overview ___ 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
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 ___ 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
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