[gmx-users] ensemble selection

fatemeh ramezani fr_750 at yahoo.com
Tue Sep 24 20:40:01 CEST 2013

 Dear Justin

I'm simulating gold nanoparticle interaction with protein by OPLSAA forcefield. I'm confused for selection an ensemble for my md run. I did energy minimization by NPT . then I did the MD by NVT. I did it because of studying of two paper that were similar to my project (Adsorption of histidine and histidine-containing peptides on Au(1 1 1):A molecular dynamics study by Zhen Xu, Shi-Ling Yuan and Interaction of b-Sheet Folds with a Gold Surface by Martin Hoefling, Susanna Monti, Stefano Corni).

But in manual and tutorials of gromacs  is proposed energy minimization should be done by NVT and NPT and then MD should be done with NPT ensemble.
in your idea should  I repeat my MD run by NPT ensemble? what is the difference of my result  between this two?

thank you

Fatemeh Ramezani

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