[gmx-users] generalized order parameters S2

Justin A. Lemkul jalemkul at vt.edu
Tue Mar 3 04:32:00 CET 2009

Dechang Li wrote:
> Dear all, 
>     I have run a 100ns simulation of protein. I want to calculate the 
> generalized order parameters S2 for N-H. It was said that to calculate
>  S2, the overall motion should be subtracted first. How can I subtract
> the overall motion? Can I use the command 'trjconv' to fit the protein 
> to a reference strucutre firstly, and then calculate S2 using command 
> 'g_rotacf'? If YES, what the reference structure is? The average
> structure in the trajectory? 

trjconv -s -f -fit will use the structure in the .tpr file as the reference. 
Try that with g_rotacf and see if you get reasonable results.  There are quite a 
few discussions and references that may be useful if you search the list archive 
for "trjconv g_rotacf."


> Best regards,
> 2009-3-3
> ========================================= 
> Dechang Li, Ph.D Candidate
> Department of Engineering Mechanics
> Tsinghua University
> Beijing 100084
> P.R. China 
> Tel:   +86-10-62773574(O) 
> Email: lidc02 at mails.tsinghua.edu.cn
> =========================================
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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