VMD-L Mailing List

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Tue Oct 27 2009 - 15:13:10 CDT

i'd like to add to discussion that i also have sometimes "stride"
failing on simulation systems (loaded as psf/dcd pairs) that ran
nicely with "namd".

On Tue, Oct 27, 2009 at 2:18 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Tue, 2009-10-27 at 13:42 -0400, Bob Johnson wrote:
>> Well...the trajectory is from a replica exchange simulation. Thus,
>> there are
>> discontinuities in the trajectory where the protein coordinates change
>> rapidly. I have all the coordinates aligned the best I can (i.e. the
>> center
>> of each protein configuration is situated close to the origin), but
>> the
>> rapid jumps are still going to be there.
>
> bob,
>
> this error happens whenever stride fails. if i remember correctly,
> it also fails when you have "unusual" hydrogen bonds. if you are
> looking at the higher temperature replica, this could be an explanation.
>
> cheers,
>   axel.
>
>>
>> I'm not sure what you mean by "large magnitude atom coordinates".
>> Thanks,
>> Bob
>>
> --
> Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
> 

-- 
Roman Petrenko
Physics Department
University of Cincinnati