[gmx-users] Increase of 5-helix count

Sundari sundi6170 at gmail.com
Mon Jun 11 14:09:39 CEST 2018

Dear gromacs users,

I am running a simulation of three alpha helical peptides with a carbon
nano tube in a simulation box. Actually I am following a paper and want to
reproduce the results.

In my simulation every time there is a sudden increase of 5-helix count,
means most of the alpha helix converted into 5-helix.

I am using gromacs version 5.1.2.  and paper used gromacs version 4. So I
am confuse is this difference I am getting because of Gromacs version or
 something else?
And  5-helix is not counted in total secondary structure count.
please suggest something.

Thank you in advance..

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