From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jul 25 2005 - 13:50:03 CDT
Joshua,
Let us know if you still need help with this. I should have a
current build of catdcd on an AIX box here if you want to try one of ours.
John
On Fri, Jul 22, 2005 at 05:04:00PM -0400, Joshua D. Moore wrote:
> Phil,
>
> I am getting caddcd to compile, but it still isn't writing the unit cell
> information. It is just skipping it. To the best of my knowledge it is
> writing the coordinates out correctly. Unless it writes the unit cell
> information differently than it did in the original NAMD output (CHARMM
> format)? I am trying to compile it on IBM - AIX 5.2 at the SDSC
> supercomputing center. I am using the VMD plugins found from
> http://www.ks.uiuc.edu/Research/namd/libraries/plugins/plugins-AIX4.tar.gz
>
> I am using the catdcd source code from
>
> http://www.ks.uiuc.edu/Development/MDTools/catdcd/files/catdcd-3.0.tar.gz
>
> My Makefile is:
>
> CC = gcc
> CFLAGS = -lm
> PLUGINDIR = /dsgpfs2/jdmoore/plugins
> ARCH = AIX4
>
> catdcd.$(ARCH): catdcd.c
> $(CC) $(CFLAGS) -I$(PLUGINDIR)/$(ARCH)/catdcd.c
> -L$(PLUGINDIR)/$(ARCH)/ -lmolfile-plugin -o $@ -lm
>
> clean:
> rm -f catdcd.o catdcd.$(ARCH)
>
> My plugin files:
>
> importgraphics_plugin.h
> libmolfile_plugin.a
> libmolfile_plugin.h
> molfile_plugin.h
> vmdplugin.h
>
> all are located in /dsgpfs2/jdmoore/plugins/AIX4 directory.
>
> Can anyone tell me what I am doing wrong? Or can someone give me updated
> VMD plugin files for AIX ? Or can someone give me the updated source code
> for the VMD plugin files? I cannot find it?
>
> Thanks.
>
> Joshua Moore
>
>
>
> On Fri, July 22, 2005 3:08 am, Philip Fowler wrote:
> > Hi Joshua,
> >
> > The trick is to recompile catdcd for which you need a set of VMD
> > plugins (for the DCDreader). I found that any set would work - in
> > fact the most recent are best because the DCDreader is much faster.
> > But, if you use the most recent set you need to add "-lm" to CFLAGS
> > in the makefile to invoke the maths libraries otherwise they won't
> > compile. Once you know this, it is pretty simple!
> >
> > My DCDunitcell info is now preserved when I merge DCD files.
> >
> > --Phil
> >
> >
> >
> >> Hi Phil,
> >>
> >> I am having this same problem now. I saw that you were able to fix
> >> it.
> >>
> >> Could you tell me the version of the VMD plugins and the version of
> >> CatDCD
> >> that you are using?
> >>
> >> My unit cell information is not even showing up in the DCD file
> >> after I
> >> put it through catdcd. It is there before in the original NAMD
> >> output I
> >> am sure.
> >>
> >> Thanks.
> >>
> >> Josh Moore
> >>
> >> On Mon, June 27, 2005 6:07 am, Philip Fowler wrote:
> >>
> >>> Hi all,
> >>>
> >>> I am calculating densities from an NPT run using VMD and therefore
> >>> need to
> >>> know the unit cell dimensions for each frame of my DCD.
> >>>
> >>> All my DCDs where run in NAMD with DCDUnitCell on. I can load a
> >>> single DCD
> >>> into VMD and retrieve the unitcell info via
> >>>
> >>>
> >>>> molinfo top get a
> >>>>
> >>>
> >>> But, if I load summary DCD that I have made using catdcd then this
> >>> information
> >>> has been lost. Yet, I see from Justin's catdcd 3.0 post
> >>>
> >>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/2150.html
> >>>
> >>> that catdcd is aware of this info and should retain it. Although I
> >>> was
> >>> sure I
> >>> used catdcd3.0, I tried again with a fresh binary and still the
> >>> info was
> >>> lost. I have also tried with no -stride set, but that made no
> >>> difference.
> >>>
> >>> Can anyone shed any light or come up with an alternative approach
> >>> (that
> >>> won't
> >>> drive me too crazy)?
> >>>
> >>> Chz,
> >>>
> >>> --Phil
> >>>
> >>>
> >>> --
> >>> Philip Fowler,
> >>> PhD Student
> >>> Centre for Computational Science,
> >>> UCL Chemistry
> >>>
> >>>
> >>
> >>
> >> --------------------------------------------------
> >> Joshua D. Moore
> >> Graduate Student
> >> North Carolina State University
> >> Department of Chemical and Biomolecular Engineering
> >> Box 7905 Centennial Campus
> >> Engineering Building I
> >> 911 Partners Way
> >> Raleigh, NC 27695-7905
> >> Phone: (919) 513-2051
> >> Fax: (919) 513-2470
> >> Email: jdmoore_at_unity.ncsu.edu
> >> --------------------------------------------------
> >>
> >>
> >
> >
>
>
> --------------------------------------------------
> Joshua D. Moore
> Graduate Student
> North Carolina State University
> Department of Chemical and Biomolecular Engineering
> Box 7905 Centennial Campus
> Engineering Building I
> 911 Partners Way
> Raleigh, NC 27695-7905
> Phone: (919) 513-2051
> Fax: (919) 513-2470
> Email: jdmoore_at_unity.ncsu.edu
> --------------------------------------------------
-- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns_at_ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
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