[AMBER] : : : : timecorr

From: Hongyi WU <why0713.sjtu.edu.cn>
Date: Sun, 28 Jul 2013 16:42:59 +0800

Dan,

Can I conduct this dynamic cross-correlation map for some (mass) centers?
I tried something like this:
matrix correl name correlation :1.N,CA,:2@,CA,CB out correl.matrix
But I get the correlation separately for each atom, not their center.

Sorry to bother you with this. ^_^

-----ʼԭ-----
: Daniel Roe [mailto:daniel.r.roe.gmail.com]
ʱ: 2013728 0:30
ռ: AMBER Mailing List
: Re: [AMBER] : : : timecorr

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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jul 28 2013 - 02:00:02 PDT
Custom Search