Re: [AMBER] : : : : timecorr

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Tue, 30 Jul 2013 21:29:59 -0600

Hi,

On Sun, Jul 28, 2013 at 2:42 AM, Hongyi WU <why0713.sjtu.edu.cn> wrote:
> Can I conduct this dynamic cross-correlation map for some (mass) centers?

Not yet. Your best bet is probably to calculate the actual vectors
with the 'vector' command, then write a script that will do the math
with the vector output.

-Dan

> 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)
>
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-- 
-------------------------
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 Tue Jul 30 2013 - 21:00:02 PDT
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