[gmx-users] using the correct .rtp files
David L. Bostick
dbostick at physics.unc.edu
Thu Jun 19 17:54:01 CEST 2003
oops... responding too quickly..
sounds like you have something set somewhere else. All I can suggest then
is to check to make sure $GMXDATA points to the right place before
grommpping.
echo $GMXDATA
if you source the GMXRC file in your .cshrc or something, you might get
GMXDATA pointing to the new version upon opening a new shell. Also check
your include line in your input mdp file...
i.e.
include = -I$GMXDATA/top -I/$GMXDATA/my_ffields
etc...
Hope it helps.. sorry for not reading carefully
David
-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
David Bostick Office: 262 Venable Hall
Dept. of Physics and Astronomy Phone: (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall dbostick at physics.unc.edu
Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
On Thu, 19 Jun 2003, Paul Barrett wrote:
> Thanks David.
>
> What do you make of the experience I described in the background that
> shows the GMXDATA variable does not seem to work.
>
> Paul
>
> >
> >Hi,
> >
> >setenv GMXDATA directory_name
> >
> >where directory_name = old /share directory from previous gmx installation.
> >
> >David
> >
> >-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> >David Bostick Office: 262 Venable Hall
> >Dept. of Physics and Astronomy Phone: (919)962-0165
> >Program in Molecular and Cellular Biophysics
> >UNC-Chapel Hill
> >CB #3255 Phillips Hall dbostick at physics.unc.edu
> >Chapel Hill, NC 27599 http://www.unc.edu/~dbostick
> >=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
> >
> >On Thu, 19 Jun 2003, Paul Barrett wrote:
> >
> >> Hi
> >>
> >> Summary:
> >> --------
> >>
> >> What is the (environment?) variable I need to change to get a new
> >> installation of GROMACS to use the /top files from a previous
> >> installation. (I may not edit the /top files from the new
> >> installation.)
> >>
> >> i.e. How do I redirect GROMACS to look in my old /top directory for .rtp
> >> files
> >>
> >> Background
> >> ----------
> >>
> >> I have been using GROMACS for a while successfully.
> >>
> >> I now want to run a version of GROMACS owned by another group. By
> >> sourcing the appropriate GMXRC my machine correctly runs using the new
> >> copy of the program
> >>
> >> However I want to continue to use the old files from /top , for example
> >> ffGMX43a1.rtp which I have edited.
> >>
> >> I thought it would be a case of setenv $GMXDATA to the directory that
> >> contains /top, however this does not work: e.g. pdb2gmx continues to
> >> refer to the /top files in the new installation.
> >>
> >> Indeed if I change $GMXDATA to somewhere altogether wrong pdb2gmx
> >> continues to use the /top from the new installation.
> >>
> >> I have got it to work by copying the .rtp (etc) files in to the
> >> directory where I am running pdb2gmx but this is not an acceptable long
> >> term solution for me.
> >>
> >> How do I redirect GROMACS to look in my old /top directory?
> >>
> >> many thanks
> >>
> >> Paul Barrett
> >> University of Oxford
> >> _______________________________________________
> >> gmx-users mailing list
> >> gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> Please don't post (un)subscribe requests to the list. Use the
> >> www interface or send it to gmx-users-request at gromacs.org.
> >>
> >
> >_______________________________________________
> >gmx-users mailing list
> >gmx-users at gromacs.org
> >http://www.gromacs.org/mailman/listinfo/gmx-users
> >Please don't post (un)subscribe requests to the list. Use the
> >www interface or send it to gmx-users-request at gromacs.org.
> >--------------------------------------------------------------------------------
> >Return-Path: <gmx-users-admin at gromacs.org>
> >Received: by biop.ox.ac.uk (MX V4.2 AXP) with SITE; Thu, 19 Jun 2003 16:41:03
> > +0100
> >Received: from oxmail.ox.ac.uk by nutmeg.biop.ox.ac.uk (MX V4.2 AXP) with SMTP;
> > Thu, 19 Jun 2003 16:41:02 +0100
> >Received: from hawk.theophys.kth.se ([130.237.25.19]) by oxmail.ox.ac.uk with
> > smtp (Exim 4.14) id 19T1X4-0007EB-4j for barrett at biop.ox.ac.uk; Thu,
> > 19 Jun 2003 16:41:02 +0100
> >Received: (qmail 17285 invoked from network); 19 Jun 2003 15:41:03 -0000
> >Received: from localhost (HELO hawk.theophys.kth.se) (127.0.0.1) by 0 with
> > SMTP; 19 Jun 2003 15:41:03 -0000
> >Received: (qmail 17250 invoked from network); 19 Jun 2003 15:40:28 -0000
> >Received: from phobos.physics.unc.edu (152.2.5.7) by 0 with SMTP; 19 Jun 2003
> > 15:40:28 -0000
> >Received: from prometheus.physics.unc.edu (prometheus.physics.unc.edu
> > [152.2.5.64]) by phobos.physics.unc.edu (8.12.3/8.12.3) with SMTP id
> > h5JFcUoE000477 for <gmx-users at gromacs.org>; Thu, 19 Jun 2003 11:40:05
> > -0400 (EDT)
> >Received: from tiberius.physics.unc.edu ([152.2.5.28]) by
> > prometheus.physics.unc.edu (SAVSMTP 3.1.0.29) with SMTP id
> > M2003061911400420427 for <gmx-users at gromacs.org>; Thu, 19 Jun 2003
> > 11:40:04 -0400
> >Message-ID: <Pine.GSO.4.33.0306191138330.17972-100000 at tiberius.physics.unc.edu>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
>
More information about the gromacs.org_gmx-users
mailing list