[gmx-users] g_hbond and contact

[Justin Lemkul]

On 3/4/13 12:04 PM, Kavyashree M wrote:
> Sir,
>
>>From Index file which gives the unique contacts -
> First section the list of atoms I want to analyse

When measuring contacts, you don't measure one group, you measure the number of 
contacts that occur between groups A and B, which considers all atoms in those 
two groups.

> [ C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ]
>
> second section : the unique contacts of each atoms with others

You don't define contacts in an index group, you define atoms that may or may 
not make contacts with others.

> [ contacts_C_CA_CB_CD_CD1_CD2_CE_CE1_CE2_CE3_CG_CG1_CG2_CZ_CZ2_CZ3_CH2 ]
>        5      7ws
>        5     10
>        5     14
>        5     18
>        5     22
>        5     24
>        5     27
>        5     30
>        5     35
>        5    292
>        5    296
>        5    30
>

There's something very wrong with this index file.  How did you generate it? 
The presence of a repeated atom number (5) and a nonsensical one (7ws) leads me 
to believe that you've done something incorrect.  Did this come from g_hbond? 
It looks like the output of -hbn, which is only useful for decoding hbmap.xpm, 
nothing else.

>>From this second section Total contacts was extracted for each atom and
> compared with
> that from a second simulation.
> These contacts was matching with the contacts of the 3rd column from
> g_mdmat output -
> @ legend string 0 "Total/mean"
> @ legend string 1 "Total"
> @ legend string 2 "Mean"
> @ legend string 3 "# atoms"
> @ legend string 4 "Mean/# atoms"
> #res    ratio  tot      mean  natm  mean/atm
>    1     1.001   11    10.991    1    10.991
>    2     1.244   10     8.041    1     8.041
>    3     1.166   13    11.147    1    11.147
>    4     1.036   11    10.615    1    10.615
>
>
> While the time dependent contacts in the xvg file shows that the first
> simulation has more
> contacts than the second one..
>

That shouldn't be unexpected.  Two independent simulations have no guarantee of 
doing the same thing, that's why sampling is so important.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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