[gmx-users] No Distribution?

[Justin Lemkul]

On 11/2/13 6:50 PM, Xu Dong Huang wrote:
> @ Gromacs users,
>
> so I did g_dist , and I’m confused by a couple of things. 1) why is it asking me for 2 groups? I have my particles of interest under 1 type, namely [ O1 ] 1    2    3, and nothing else. 2) I just picked the same group twice, and the result is gives me in xvg is the following
> There are no distances measured, that cannot be right.
>

You can't just hope for magic.  Please read g_dist -h to understand what the 
program is doing.  Like I said, you have to measure each distance manually, i.e. 
individually.  You need three index groups:

[ 1 ]
1
[ 2 ]
2
[ 3 ]
3

Then measure the distances between 1&2, 2&3, and 1&3.  Post-process each 
individually to get the distributions or pool the data (cat the resulting files) 
and get the distribution from that, if it is in any way meaningful.

>     0.0000000    0.0000000    0.0000000    0.0000000    0.0000000
>    20.0000000    0.0000000    0.0000000    0.0000000    0.0000000
>    40.0000000    0.0000000    0.0000000    0.0000000    0.0000000
>    60.0000000    0.0000000    0.0000000    0.0000000    0.0000000
>    80.0000000    0.0000000    0.0000000    0.0000000    0.0000000
>   100.0000000    0.0000000    0.0000000    0.0000000    0.0000000
>   120.0000000    0.0000000    0.0000000    0.0000000    0.0000000
>   140.0000000    0.0000000    0.0000000    0.0000000    0.0000000
>   160.0000000    0.0000000    0.0000000    0.0000000    0.0000000
>   180.0000000    0.0000000    0.0000000    0.0000000    0.0000000
>   200.0000000    0.0000000    0.0000000    0.0000000    0.0000000
>   220.0000000    0.0000000    0.0000000    0.0000000    0.0000000
>   240.0000000    0.0000000    0.0000000    0.0000000    0.0000000
>   260.0000000    0.0000000    0.0000000    0.0000000    0.0000000
> …

Makes sense; the distance between any one group and itself is zero.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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