[gmx-users] g_hbond and contact

[Kavyashree M]

Sir,

>From Index file which gives the unique contacts -
First section the list of atoms I want to analyse
[ 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
[ 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

>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..

I hope I am clear this time.

Thank you
kavya

On Mon, Mar 4, 2013 at 10:05 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 3/4/13 11:25 AM, Kavyashree M wrote:
>
>> Dear users,
>>
>> I used the following tool for finding the contacts
>> g_hbond_46 -f a.xtc -s a.tpr -contact -n a.ndx -r 0.4 -hbm a.xpm -hbn
>> a.ndx
>> -num a.xvg
>>
>>> From the index file, the number of contacts of each atom was extracted.
>>>
>> This and the
>> xvg output was compared with another simulation.
>> It was found that the number of contacts was more in 2nd simulation
>> compared to
>> the first. But When I compared xvg file it was showing the opposite
>> behaviour.
>>
>
> These statements don't make any sense.  How did you determine that the
> number of contacts in simulation 2 was greater than simulation 1, but then
> the .xvg files showed the opposite?  The number of contacts come from the
> .xvg files?  Perhaps you simply swapped your files during analysis.
>
>
>  The contacts was also calculated using g_mdmat for the same cutoff and it
>> was agreeing
>> with the numbers I got from in index output of g_hbond.
>>
>> Why is this difference in index and xvg output?
>>
>
> An index group is a list of atom numbers.  The .xvg output is whatever you
> tell it to be, in this case, the number of contacts within the group
> selected.
>
> -Justin
>
>
>  Also the xvg file looks like -
>>
>> s0 legend "Contacts"
>> @ s1 legend "Pairs within 0.4 nm"
>>        4000        7496           0
>>        4002        7513           0
>>        4004        7605           0
>>        4006        7531           0
>>        4008        7573           0
>>        4010        7546           0
>>        4012        7544           0
>>        4014        7526           0
>>        4016        7530           0
>>        4018        7496           0
>>        4020        7526           0
>> ..
>>
>>
>> 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>
>
> ==============================**==========
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