[gmx-users] Free energy change calculation

[Xiaotong Zhang]

Hi,

Sorry to bother you. Recently, I have encountered a problem when running free energy calculation of a dna-ligand complex system. The structure start to getting weird when I try to specify the two state (A,B) in the topology file, which is never spotted in the unconstrained MD simulations.

The version I am using is 4.6.7 and the force constant is 1000/nm/rad^2.

Could you help me with that?

Cheers

Xiaotong

Xiaotong Zhang
PGR student
xz41 at st-andrews.ac.uk<mailto:xz41 at st-andrews.ac.uk>
School of Chemistry, University of St Andrews
Purdie Building, North Haugh
St Andrews, KY16 9ST