AMBER Archive (2009)

Subject: Re: [AMBER] ptraj utility

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Dec 01 2009 - 06:48:27 CST

maybe it's a multimer and there is periodic imaging going on?

On Tue, Dec 1, 2009 at 7:45 AM, Daniel Roe <droe_at_nist.gov> wrote:

> It's difficult to answer your question without some more information about
> your system. I assume that since you mentioned a box this is a periodic
> system, but what does your ptraj input look like, what kind of molecule did
> you simulate and how big, etc.
>
> The easiest thing for you to do would probably be to look at those frames
> of the trajectory yourself using your favorite visualization program and see
> if those distances make sense. Depending on your system, it's not
> inconceivable that you're sampling some sort of transient event (e.g.
> partial unfolding in a peptide) that is causing your distance to spike.
>
> Hope this helps,
>
> -Dan
>
> Neha Bharat Gajaria wrote:
>
>> Hi List,
>>
>> I m trying to extract the distance between two Calpha atoms from amber
>> trajectories using ptraj. The average distance should be 10.05 Ang. After
>> 50ns or so, the distances reported in the output are very unusual.
>>
>> The output looks like
>> 9.45
>> 9.85
>> .
>> .
>> .
>> 40.23
>> 33.12
>>
>> .
>> .
>> .
>> 8.10
>> 8.93
>>
>> Are some of the trajectories corrupted or something is going wrong with
>> the
>> box? thanking you for your response
>>
>>
>>
>
> --
> Daniel R. Roe, Ph.D.
> Research Chemist
> National Institute of Standards and Technology
> 100 Bureau Drive, Stop 8443
> Gaithersburg, MD 20899-8443
> (301) 975-8741
>
>
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