(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


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.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(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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