Hi,
That is certainly strange. Have you visualized the trajectory at those
exact frames? Do the structures look corrupted in any way? Also, have
you tried using cpptraj - does it have the same issue?
-Dan
On Tue, Feb 14, 2012 at 10:40 AM, Giachetti Andrea - CERM
<giachetti.cerm.unifi.it> wrote:
> I'm calculating the distance from two atoms, the trajectory is without
> solvent and I use netcdf files as input.
> The figure show the distance of two atoms during the trajectory.
>
> Andrea
>
>
> On 02/14/2012 04:24 PM, Daniel Roe wrote:
>>
>> Hi,
>>
>> On Tue, Feb 14, 2012 at 9:54 AM, Giachetti Andrea - CERM
>> <giachetti.cerm.unifi.it> wrote:
>>>
>>> Hi all, I'm trying to extract coordinates from amber trj trajectory
>>> file, but there are some steps with discontinuities (jumps). Could it be
>>> related to periodic boundary conditions ?
>>
>> What exactly do you mean by discontinuities? Are they in something you
>> are calculating (i.e. distance, RMSD, etc) or in the physical
>> coordinates of the molecule (or both?). It would probably be useful to
>> know something about the original trajectory (does it have solvent,
>> PBC, etc).
>>
>> -Dan
>>
>
>
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>
--
-------------------------
Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ 08854
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Received on Tue Feb 14 2012 - 08:00:03 PST
