[gmx-users] g_analyze doubt

[Justin A. Lemkul]

aiswarya pawar wrote:
> If i give command as =
> 
> g_dist -f md.xtc -s md.tpr -n index.ndx -dist 0.8
> 
> this prints out all the protein water distance within 0.8nm. The data printed out is such that=
> 
> t: 1466  5369 SOL 20624 OW  0.789894 (nm)
> t: 1467  5369 SOL 20624 OW  0.781596 (nm)
> t: 1469  5369 SOL 20624 OW  0.785377 (nm)
> t: 1473  5369 SOL 20624 OW  0.763485 (nm)
> t: 1474  5369 SOL 20624 OW  0.767805 (nm)
> t: 1475  5369 SOL 20624 OW  0.736003 (nm)
> t: 1476  5369 SOL 20624 OW  0.707953 (nm)
> t: 1477  5369 SOL 20624 OW  0.713135 (nm)
> t: 1478  5369 SOL 20624 OW  0.694042 (nm)
> t: 1480  5369 SOL 20624 OW  0.733907 (nm)
> t: 1481  5369 SOL 20624 OW  0.705245 (nm)
> t: 1482  5369 SOL 20624 OW  0.678473 (nm)
> t: 1483  5369 SOL 20624 OW  0.6288 (nm)
> t: 1492  5369 SOL 20624 OW  0.794252 (nm)
> t: 1496  5369 SOL 20624 OW  0.753049 (nm)
> t: 1497  5369 SOL 20624 OW  0.782796 (nm)
> t: 1498  5369 SOL 20624 OW  0.799607 (nm)
> t: 1499  5369 SOL 20624 OW  0.69987 (nm)
> t: 1500  5369 SOL 20624 OW  0.763511 (nm)
> t: 1501  5369 SOL 20624 OW  0.764072 (nm)
> t: 1502  5369 SOL 20624 OW  0.739181 (nm)
> t: 1503  5369 SOL 20624 OW  0.70336 (nm)
> 
> 
> In the above data can be seen that the time frame is not continuos. i.e. only the time at which the protein water distance within 0.8nm are shown. So is it possible to do g_analyze on this?
> 

As I said before, g_analyze can only perform statistical operations on the 
(numerical) data supplied to it.  What you've asked g_dist to do is print a list 
of any atoms that satisfy the distance criteria.  You may get frames where there 
  are none, you may get frames where there are several atoms that work.  There's 
nothing here that g_analyze can do anything with.  You can't average apples and 
oranges and hope to get grapes, though you might go bananas :) Sorry, couldn't 
resist a bit of fun there...

-Justin

> 
> On 01-Feb-2012, at 6:48 PM, Justin A. Lemkul wrote:
> 
>>
>> aiswarya pawar wrote:
>>> Dear Gromacs Users,
>>> i have data for the distance between the protein and water atoms within a cut off of 8A for 5ns using the g_dist option. Now i want to use g_analyze on this data. The time frame in the output data is not continuous because of the cut off provided. So i would like to know how would the g_analyze would compute the data.
>> I'm not clear on what you're trying to do.  g_analyze performs simple statistical operations (averages, error estimates) on the input data.  If there are discontinuities (which I do not understand the nature of), they come from the g_dist data, not what g_analyze is doing.
>>
>> Please provide a more clear description of what you are doing, including all relevant commands, and examples of the data files, if necessary.
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> 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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> 
> 

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

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

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