(unknown charset) Re: [AMBER] 答复: 答复: 答复: timecorr

From: (unknown charset) Daniel Roe <daniel.r.roe.gmail.com>
Date: Sat, 27 Jul 2013 10:29:56 -0600

Hi,

On Fri, Jul 26, 2013 at 8:53 AM, Hongyi WU <why0713.sjtu.edu.cn> wrote:
> But can I define different masks for different residues in this command?

You can't, it is by definition a symmetric matrix.

> I have already tried "crosscor", another command you mentioned to me, like
> this:
> Parm R.prmtop
> trajin R.mdcrd
> vector v1 center :1.N
> vector v2 center :2.CB
> crosscor v1 v2 out 1_2.crosscor
>
> But I get all zeros.

Unfortunately the 'crosscorr' command currently works with non-vector
data sets only. I think probably your best bet at this point is to use
'matrix correl' with a mask that encompasses all of the atoms you wish
to look at, e.g.:

matrix correl name correlation :1.N,:2.CB out correl.matrix

In this case the off-diagonal elements in 'correl.matrix' will contain
the information you want.

-Dan

-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Sat Jul 27 2013 - 10:00:02 PDT
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