[gmx-users] Removing external bias apart from umbrella potential

Sanku M msanku65 at yahoo.com
Thu Jan 17 04:17:10 CET 2013


I am recently trying to perform an umbrella sampling simulation along a particular reaction coordinate on a system where I have also put position restraint on certain atoms of the system... So, for each umbrella sampling window, I have an extra potential on certain atoms ( due to the position restraint ) apart from the umbrella potential. I am using Gromacs4.5.4 for the simulation.

So, after carrying out the umbrella sampling simulation, if I use WHAM  to remove the bias,  I think  WHAM, in its present implementation,  can only remove the bias due to the umbrella potential. But the bias required for position-restraining certain atoms remains still there in the computed PMF.

So, I was wondering whether you can suggest any way-out for removing that bias from the PMF due to position restraints  as well. 


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