[gmx-users] Umbrella sampling

Paula Andrea Delgado Pinzon pa-delga at uniandes.edu.co
Fri Aug 10 19:14:29 CEST 2012

Good morning,
I am trying to run an umbrella sampling simulation, my system is a complex of two proteins.  I have a couple of  questions:
1. i don't know which is the purpose in defining the charge of each protein end
2. When i check the topol.itp file of the reference molecule i realized that it already has 

#ifdef POSRES_B
#include "posre_B.itp"

and when i check the file of the other protein it has it too
3. I don't know how to decide the size of the unit cell and which is the criterion to center the molecules
4. I am not sure why in the equilibration step and NVT it hasn't been done
5. In the neutralization part in this kind of simulation ones has to specified the concentration of the solution or i can do it just with the number of ions i want to add

Thank you 


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