VMD-L Mailing List

From: Phelan Jr., Frederick R. Dr. (frederick.phelan_at_nist.gov)
Date: Wed Apr 20 2011 - 15:30:52 CDT

Thanks. I'll upgrade immediately and give it a try.

Fred

-----Original Message-----
From: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
Sent: Wednesday, April 20, 2011 4:26 PM
To: Phelan Jr., Frederick R. Dr.
Subject: Re: vmd-l: Generating Topo Bond Data from LAMMPS Data File

On Wed, Apr 20, 2011 at 4:14 PM, Phelan Jr., Frederick R. Dr.
<frederick.phelan_at_nist.gov> wrote:
> a) Will do except on this one ...
> b) VMD 1.8.7 and topo 1.0 ...

you need to upgrade to vmd 1,9

the problem is in the lammps molfile plugin.
it was fixed briefly before vmd 1.9 was released.
1.9 comes with tt 1.1. 1.2 has some small bugfixes.

e.g. for topo guessatom data, which is convenient for
generating .psf files for visualization.

axel.

>
> Fred
>
>
> -----Original Message-----
> From: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
> Sent: Wednesday, April 20, 2011 4:09 PM
> To: Phelan Jr., Frederick R. Dr.
> Subject: Re: vmd-l: Generating Topo Bond Data from LAMMPS Data File
>
> a) please keep the list in cc
> b) what VMD and topotools version?
>
> axel.
>
> On Wed, Apr 20, 2011 at 3:30 PM, Phelan Jr., Frederick R. Dr.
> <frederick.phelan_at_nist.gov> wrote:
>> I apologize in advance, because I am sure this is probably asked all the time, but how do I communicate the topology to the trajectory display? I am way off in my interpretation.
>>
>> I did:
>>
>>        topo readlammpsdata file.data
>>        animate write psf file.psf
>>
>> This gave me the psf file with the topology.
>>
>> I then closed and reopened vmd, read in the trajectory file, and then read in the psf with:
>>
>>        animate read psf file.psf
>>
>> However, the bonds are way off ... they were correct when I read in the lammps data file.
>>
>> Thanks,
>> Fred
>>
>>
>>
>> -----Original Message-----
>> From: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
>> Sent: Wednesday, April 20, 2011 1:22 PM
>> To: Phelan Jr., Frederick R. Dr.
>> Subject: RE: vmd-l: Generating Topo Bond Data from LAMMPS Data File
>>
>> On Wed, 2011-04-20 at 13:18 -0400, Phelan Jr., Frederick R. Dr. wrote:
>>> Is this new? writelammpsdata works, but readlammpsdata gives me "invalid command name" ...
>>
>> which version of VMD and topotools?
>>
>> a.
>>
>>> -----Original Message-----
>>> From: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
>>> Sent: Wednesday, April 20, 2011 12:18 PM
>>> To: Phelan Jr., Frederick R. Dr.
>>> Cc: vmd-l_at_ks.uiuc.edu
>>> Subject: Re: vmd-l: Generating Topo Bond Data from LAMMPS Data File
>>>
>>> On Wed, Apr 20, 2011 at 11:23 AM, Phelan Jr., Frederick R. Dr.
>>> <frederick.phelan_at_nist.gov> wrote:
>>> > The default when you read in a LAMMPS trajectory file to VMD is to display
>>> > the atoms without bonds.
>>> >
>>> >
>>> >
>>> > Is there a tool/script that generates the bond topology from the LAMMPS
>>> > ".data" file associated with the ".lammpstrj" file which can then be
>>> > incorporated using topotools?
>>>
>>> yes. and it is already well documented:
>>>
>>> http://sites.google.com/site/akohlmey/software/topotools/topotools---documentation#TOC-readlammpsdata-file-name-atom-style
>>>
>>> axel.
>>>
>>> >
>>> >
>>> >
>>> > On the topotools page
>>> > (http://sites.google.com/site/akohlmey/software/topotools/topotools-tutorial---introduction),
>>> > I see that there is information about building a LAMMPS data file from
>>> > molecular data in VMD, so essentially, this is the reverse of that process.
>>> >
>>> >
>>> >
>>> > Thanks,
>>> >
>>> > Fred
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> > ________________________________
>>> >
>>> > Frederick R. Phelan Jr., Ph.D.
>>> > Complex Fluids Group
>>> > Polymers Division
>>> > National Institute of Standards and Technology
>>> >
>>> > ________________________________
>>> >
>>> > NIST, Bldg. 224/Rm. A209
>>> > 100 Bureau Dr., STOP 8542
>>> > Gaithersburg, MD 20899-8542
>>> > 301.975.6761 (VOX)
>>> > 301.975.4924 (FAX)
>>> > Frederick.Phelan_at_nist.gov
>>> >
>>> > My Polymers Home Page
>>> >
>>> >
>>> >
>>>
>>>
>>>
>>
>> --
>> Dr. Axel Kohlmeyer
>> akohlmey_at_gmail.com http://goo.gl/1wk0
>>
>> Institute for Computational Molecular Science
>> Temple University, Philadelphia PA, USA.
>>
>>
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.