Re: [AMBER] how to calculate the mass center distance between adjacent repeat units of one polymer chain

From: 唐元晖 <tangyuanhui08.126.com>
Date: Wed, 6 Jun 2018 04:09:17 +0800 (CST)

Thank you. I have learned that. Thank you for your suggestions.

```--
Yuanhui Tang
Doctor  Candidate
Beijing Key Laboratory for Membrane Materials and Engineering
Department of Chemical Engineering, Tsinghua University
Beijing 100084, PR China
Tel: 86-10-62794742;
Email: tangyh08.gmail.com
At 2018-06-06 01:13:23, "Wesley Michael Botello-Smith" <wmsmith.uci.edu> wrote:
>I would use pytraj to this. You can accomplish the same thing using the "
>pytraj.analysis.vector.center" command
>see: http://amber-md.github.io/pytraj/latest/_api/pytraj.vector.html
>python.
>
>You could even then use pytraj.compute or pytraj.pmap if you want to do the
>loop for you. These commands can take a python style list of individual
>commands as input and will automatically run each one. The pmap command
>will even let you run them in parallel.
>
>If you really want to do this in cpptraj, you would have to write each i j
>combination explicitly. Before I learned pytraj, I would usually write a
>bash script to generate the cpptraj input script to do that sort of
>iteration.
>
>Hope that helps!
>
>On Tue, Jun 5, 2018 at 9:53 AM, 唐元晖 <tangyuanhui08.126.com> wrote:
>
>> Hello all,
>>
>>
>> This is Yuanhui. I want to calculate the distance between two residues as
>> :i and :j, and i, j can be changed during a loop. However, the distance
>> mask doesn't recognize the word :i. The input file is written like this:
>>
>>
>> parm *.prmtop
>> trajin md15.mdcrd 1 last 200
>> i=2
>> j=3
>> distance dist :i :j out dist.dat
>>
>>
>> Is there a way can make the cpptraj recognize the variable 'i' and 'j',
>> because I want to change their values.
>> Best wishes!
>>
>>
>>
>> --
>>
>> Dr. Yuanhui Tang
>> Ralph E. Martin Department of Chemical Engineering
>> University of Arkansas
>> Cato Springs Research Center
>> Fayetteville, AR 72701
>> email: yt006.uark.edu
>> voice: (479) 409-9989
>>
>>
>>
>>
>>
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Received on Tue Jun 05 2018 - 13:30:03 PDT
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