[gmx-users] residue titration w/ FEP

paloureiro at biof.ufrj.br paloureiro at biof.ufrj.br
Mon Aug 22 14:13:02 CEST 2005

> Hello,
> I am calculating the free energy for deprotonating GLU-H --> GLU.   This is
> an annihilation FEP exercise. State A is a regular GLUH residue, and State
> B is the same residue with all bonded interactions the same, but all
> non-bonded interactios turned off.  Also in state B, the mass of the proton
> is zero.
> I run into a problem at the very last window simulation at lambda=1 where
> the proton has no mass.  Basically the proton moves around wildly w.r.t.
> the residue and I get LINCS errors that cause the program to crash. I
> imagine this is because there are no forces on the proton to keep it
> tethered to the residue.
> I imagine the solution is to mutate the proton to a dummy atom, but I'm not
> sure how to do this. Could someone offer help / suggestions?
Yes, use atom "MW" or "DUM" as state B of the proton and use soft core 
(for instance, sc-alpha=1.5 and sc-sigma=0.3)
Maybe you will have to use a smaller time step, though. 



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