[gmx-users] Fwd: Regarding Umbrella samplling

Sathish Kumar sathishk238 at gmail.com
Mon Sep 29 16:24:49 CEST 2014

Dear gromacs usres,

 I have run the umbrella sampling with the help of tutorial of justin....In
my system rna is binding with gold nanoparticle...to find out the binding
energy,  i run the umbrella sampling by pulling one end of the siRNA untill
it unbind from gold nanoparticle. The snap shots obtained from pulling
simulation were used to generate configurations with the spacing 0.2 nm and
i got total 59 configurations, each configuration was run for 5 ns. The
profile files are shared with the link below.



In the profile image, i have not got the plateu value, can i take the
difference between final and starting pmf values for  the binding enrgy.
Please give suggestions.


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