[gmx-users] Gauche dihedrals fraction

[Justin A. Lemkul]

Sławomir Stachura wrote:
> Hi,
> I have simulated fully hydrated POPC membrane for 50 ns and now I am analysing if it's in equilibrated state. One of the needed by me parameters is fraction of gauche dihedrals in acyl chains.  I have tried g_angle, but it only shows fraction of trans dihedrals. So is there possibility to  calculate this parameter from trajectory? 

Use g_angle -ov -all and post-process the resulting .xvg file (which will 
contain all the instantaneous values of the dihedral angles).  Otherwise, you'd 
have to modify the code to make it do what you want.  It's probably easier to 
just write a little Perl script that runs through the angaver.xvg file (from 
-ov) and does the counting for you.

-Justin

> Best wishes,
>       Slawomir-- 
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-- 
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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

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