From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Mon Jul 25 2005 - 14:16:16 CDT
Thanks Phil,
Yes, I still haven't gotten it to work yet. A current build of catdcd on
AIX would be great. Do you also have the VMD plugins for AIX? Like I
said, I tried to ones I had, but I am getting the same problem.
Thanks again.
Josh
On Mon, July 25, 2005 2:50 pm, John Stone wrote:
>
> 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
>
--------------------------------------------------
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
--------------------------------------------------
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