Re: catdcd and dcdunitcell

From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Fri Jul 22 2005 - 16:04:00 CDT

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
--------------------------------------------------

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