VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu May 10 2012 - 13:43:31 CDT

hi,

i have now an updated version of the plugin
with multiple enhancements.
- it will read in box information
- it can read in velocity data, if present
- it can *write* correctly formatted restart files

before committing this to the CVS and thus having
it included in the next VMD release, it seems prudent
to have some testing to confirm that these changes
are compatible with existing files "in the wild" and
work on multiple platforms.

thus please, anybody that is using amber7 style
restarts and interested in testing these new features,
please contact me off-list and i'll try to ship you a
plugin update for your platform.

thanks,
     axel.

On Thu, May 10, 2012 at 10:05 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Thu, May 10, 2012 at 3:53 AM, Albert <mailmd2011_at_gmail.com> wrote:
>> Dear:
>>
>>  I am trying to load amber MD files by command:
>>
>> vmd apo.prmtop -rst7 m6.rst
>>
>> and I get the following information for above command:
>>
>> Box Dimensions are 86.454002  79.653999  100.666603  90.000000  90.000000
>>  90.000000
>>
>> when I try to type pbc box in terminal, it said:
>>
>> -error Suspicious pbc side length (a=0.000000 b=0.000000 c=0.000000). Have
>> you forgotten to set the pbc parameters?
>>
>> I also try to open periodic molecule from representation menu, but nothing
>> more displayed....
>>
>> I am wondering what happen?
>
> very simple. this plugin was apparently written before
> the VMD molfile API supported importing box dimension
> information and never revised for that later on.
>
> this needs to be fixed in the plugin source, but since
> there is code to detect this already in place, it should
> not be too difficult to add this.
>
> what platform are you running VMD on?
> can you send me a few small test files?
>
> axel.
>
>>
>> thank you very much
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com  http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA. 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.