[gmx-users] g_hbond and contact

[Justin Lemkul]

On 3/4/13 1:10 PM, Kavyashree M wrote:
> 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.
>
>

OK, then I still don't know what "7ws" is, but the only purpose for this file is 
to provide a key to the existence matrix in hbmap.xpm.  Your previous 
description indicated that you were using it for some other analysis, which 
would not be appropriate.

The other thing worth mentioning here is something that was posted to the list 
just a few hours ago, that the output of g_hbond -contact may not agree with 
other methods of calculating contacts, especially in the case of -merge vs. 
-nomerge.

-Justin

>>
>>   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
>

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

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

========================================