[gmx-users] g_hbond and contact

[Kavyashree M]

On Mon, Mar 4, 2013 at 11:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
> 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.
>

I gave a group of hydrophobic atoms in both cases
The command I gave -
g_hbond_46  -f    x.xtc    -s   x.tpr    -contact   -n   x.ndx   -r   0.4
-hbm   o.xpm   -hbn   o.ndx   -num   o.xvg
my index file contained a group of hydrophobic atoms. which I supplied in
the x.ndx.


>
>  You don't define contacts in an index group, you define atoms that may or
> may not make contacts with others.
>
>
The one I mentioned here is the output index file from the g_hbond (4.6
version) - o.ndx.


>
>  [ 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.
>
>
I did not generate this. The tool (g_hbond) generated this index file. It
is the -hbn output.


>
>  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.
>

Thank you
kavya