[gmx-users] end-to-end distance

[Justin A. Lemkul]

Zuzana Benkova wrote:
> Dear Justin,
> 
> thank you for response and I am sorry not to define my problem properly. 
> I have used the first alternative, which you discribed and thus obtained 
> the weird resluts. Before I used this alternative I did what you 
> mentioned as the second alternative if I understood it correctly. I have 
> specified the first and the last atoms of each chain as separate groups. 
> But this makes 64 pairs of groups for 64 chairs and I need to apply 64 
> times g_dist, please, could you correct me if I am wrong? If I am right 
> than it is better to write a script.
> 

Scripting is indeed your friend here.  The first groups you've shown will simply 
be used to find the COM of each group and measure the COM distance as a function 
of time; g_dist does not attempt to intelligently split up the group and do what 
you want.

-Justin

> I am appending the example of my group definitions
> 
> [ PEO1_&_CH3 ]
> 1   87  173  259  345  431  517  603  689  775  861  947 1033 1119 1205
> 1291 1377 1463 1549 1635 1721 1807 1893 1979 2065 2151 2237 2323 2409 2495
> 2581 2667 2753 2839 2925 3011 3097 3183 3269 3355 3441 3527 3613 3699 3785
> 3871 3957 4043 4129 4215 4301 4387 4473 4559 4645 4731 4817 4903 4989 5075
> 5161 5247 5333 5419
> [ PEON_&_CH3 ]
> 83  169  255  341  427  513  599  685  771  857  943 1029 1115 1201 1287
> 1373 1459 1545 1631 1717 1803 1889 1975 2061 2147 2233 2319 2405 2491 2577
> 2663 2749 2835 2921 3007 3093 3179 3265 3351 3437 3523 3609 3695 3781 3867
> 3953 4039 4125 4211 4297 4383 4469 4555 4641 4727 4813 4899 4985 5071 5157
> 5243 5329 5415 5501
> 
> which provided weird results
> 
> [ R1 ]
> 1
> 
> [ R11 ]
> 83
> 
> [ R2 ]
> 87
> 
> [ R22]
> 169
> 
> till [ R64 ] [ R6464 ] pairs which step-by step gave realistic results.
> 
> Thank you in advance
> 
> Zuzana.
> 
> 
> 
> Dňa 02/18/10, *"Justin A. Lemkul" * <jalemkul at vt.edu> napísal:
>>
>>
>> Zuzana Benkova wrote:
>> >Dear GROMACS users,
>> >
>> >I have a system of 64 chains and want to calculate averaged values of 
>> end-to-end distance of all chains as well as the averaged radius of 
>> gyration from 1ns trajectory. In the case of end-to-end distance I 
>> have prepared index file containing one group of the first atoms in 
>> ascending order and the second one containing the terminal atoms in 
>> ascending order. I have used g_dist but it looks like it combined all 
>> pairs between both groups. I have looked at the mailing list but did 
>> not find the answer.
>> >
>>
>> g_dist should only be measuring the COM distance between the two 
>> selected groups, so I don't know what you mean by "combined all pairs" 
>> - perhaps you can provide an example (index groups, relevant output, 
>> what you were expecting, and why you think it's wrong)?  If your 
>> groups contain all starting residues in one, then all ending residues 
>> in another, then yes, you're going to get weird results.  If you have 
>> one chain that is residues 1-100, you should have a group for r_1 and 
>> a group for r_100; select those for g_dist analysis.  If another chain 
>> is residue 101-200, r_101 and r_200 are what you want, etc.
>>
>> >Is it possible to do such analysis using directly GROMACS tools or I 
>> need to prepare some scripts with loops running over all chains. Thank 
>> you for response in advance.
>> >
>>
>> It certainly should be possible to iteratively use g_dist to measure 
>> distances between whatever groups you select.  Fairly straightforward, 
>> actually, so if you're not getting what you expect, provide the 
>> information I asked for above and hopefully someone should be able to 
>> figure out what's going wrong.
>>
>> -Justin
>>
>> >Zuzana Benkova
>> >
>>
>> -- 
>> ========================================
>>
>> 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

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