VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Aug 23 2011 - 10:18:00 CDT

On Tue, Aug 23, 2011 at 11:13 AM, Moeed <lecielll_at_googlemail.com> wrote:
> Hello Sir,
>
> Thank you. Here is what I do:
>
> load gro file.
> load trr or xtc file ( frames from 1 to 500, "stride" 1, "load all at
> once").
> drawing method: Type or CPK
>
> problem: artificial bonds viewed

those bonds are _not_ artificial.
it is only that your atoms have moved
across periodic boundaries (or rather
the .trr file has a different center than
the .gro file).

the cure for this is to use the pbctools
plugin and "unwrap" your trajectory like
it has been discussed on this very mailing
list many, many times. thus if you have questions,
about pbctools, please first thoroughly search
the mailing list archives. most likely your
(future) questions have already been answered
(in the past). ;)

cheers,
   axel.

>
> I have attached the starting structure as well as an image which shows the
> problem. I am guessing that is because of the PBC.
>
> Thank you,
>
> On Tue, Aug 23, 2011 at 10:30 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Tue, Aug 23, 2011 at 6:49 AM, Moeed <lecielll_at_googlemail.com> wrote:
>> > Hi John,
>> >
>> > Thanks. Yes, I am using gro. file which uses nanometers. This means
>> > every
>> > time I have to change the units?
>>
>> no. all plugins for gromacs based file formats transparently
>> convert between nanometers and angstroms.
>>
>> please provide an example showing what exactly
>> your problem is.
>>
>> axel.
>>
>> > On Mon, Aug 15, 2011 at 12:21 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>> >>
>> >> Hi,
>> >>  This is usually caused by problems with the interpretation of the
>> >> coordinate units in the files being loaded.  Is it possible that you've
>> >> got your atomic coordinates in units of nanometers, but have saved them
>> >> to a file format (e.g. PDB) that expects Angstroms?
>> >>
>> >> Cheers,
>> >>  John Stone
>> >>  vmd_at_ks.uiuc.edu
>> >>
>> >> On Mon, Aug 15, 2011 at 12:09:51PM -0400, Moeed wrote:
>> >> >    Hello all,
>> >> >
>> >> >    I have a problem visualizing my structure in vmd. Once I load
>> >> > structure
>> >> >    and trajectory files file I see some artificial bonds connecting
>> >> > all
>> >> > atoms
>> >> >    while there is no bond between them. Has anyone any ideas why this
>> >> > is
>> >> >    happening?
>> >> >
>> >> >    Thank you,
>> >>
>> >> --
>> >> NIH Resource for Macromolecular Modeling and Bioinformatics
>> >> Beckman Institute for Advanced Science and Technology
>> >> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> >> http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
>> >> http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078
>> >
>> >
>>
>>
>>
>> --
>> 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.