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Hi all.
I’m new to gromacs, and I would be glad to get some advice from more experienced usres. I would like to estimate the difference in free energy between two systems. First system (A) consists of DPPC membrane, TM-protein and some Zn ions interacting with the protein. Second (B) has the same elements but Zn ions are far away from the protein (in the solvent). Is it possible to estimate free energy difference between those two systems in gromacs? I thought about using dummy atoms and slow-growth methods for free energy calculations. During the simulation, Zn ions from system (A) would be perturbated into dummy atoms (charge=0, mass = 0) and at the same time equal number of dummy atoms in the solvent would be perturbated to Zn atoms? Is it possible to achieve? For the beginning I tried to estimate the difference in free energy between two systems. 1) first system consisted of two Cl- and one Zn2+ ions + solvent 2) second only solvent molecules During the 100 ps MD I perturbated chare and mass of Cl and Zn ions to zero. The energy values that I’ve obtained are wrong 960200,46. I’m new to gromacs so I would appreciate your help a lot. Here are my input files (I’m using ffgmx ) --------------md.mdp-------------
pp
=
/lib/cpp
define = -DFLEX_SPC constraints = none integrator = md dt = 0.001 nsteps = 100000 nstxout = 100000 nstvout = 100000 nstfout = 100000 nstlog = 100 nstenergy = 100 nstxtcout = 100 nstlist = 10 ns_type = grid rlist = 1.0 free_energy = yes init_lambda = 0 delta_lambda = 0.00001 sc-alpha = 1.5 sc-sigma = 0.3 .... ...
....
---------------------------------------
--------ZN.itp-----------------------
[ moleculetype ]
; molname nrexcl ZnB 1 [ atoms ]
; id at type res nr residu name at name cg nr charge typeB chargeB massB 1 Zn 1 Zn Zn 1 2 65.37000 Zn 0 0 ---------------------------------------
-----------Cl.itp-----------------
[ moleculetype ]
; molname nrexcl ClB 1 [ atoms ]
; id at type res nr residu name at name cg nr charge typeB chargeB massB 1 Cl 1 Cl Cl 1 -1 35.45300 Cl 0 0 ----------------------------
THANK YOU FOR HELP
All the best.
:)
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