[gmx-users] g_hbond and contact

[Kavyashree M]

I am sorry There is no "7ws" Its a typographic error. What I wanted to ask
was -
I am comparing two simulations S1 and S2 for contacts at a given cut off
I used g_mdmat and g_hbond to calculate it.
g_hbond outputs: of "-num" and "-hbn" was considered.
            1. -hbn output was analysed to calculate how many contacts each
                atom has from both  S1 and S2.
            2. -num output graph was compared from both S1 and S2.
g_mdmat output: of "-no" was considered.
            3. -no output was analysed from both S1 and S2 using the
                third column or the second Y value which gives total
contacts
                of each atom.

It was observed that "1" and "3" matched exactly giving the same number of
contacts each atom has (in the whole simulations). indicating that the
number
of contacts each atom has was more in S2 than S1.

But the graph from "2" indicated that the number of contacts (along the
trajectory)
in S1 was higher than S2.

My doubt is:
The number of contact per atom follows S2 > S1
while number of contacts per time follows S1 > S2.
I am unclear as to what I  have to conclude from this observations.

-----> I used the same cutoff throughout.
-----> There has not been any swapping of the trajectory while analysing.

Thank you
Kavya


On Tue, Mar 5, 2013 at 1:09 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>