[gmx-users] Topology file (type A type B format) for free energy calculation of bond breaking

deepak bapat dubapat at gmail.com
Wed Oct 11 09:18:28 CEST 2017

Dear Gromacs Users

I wish to calculate free energy simulation in which I wish to break bond
within a molecule from state A to state B.

If I use bond type 6 to define that bond in the molecule then i think it
should not generate exclusions  (as stated in the manual of Gromacs version
5.1.2, section 5.4.4.  I checked this with gmx dump -f md.tpr as well)

; a1   a2    la       ka    kb  kb
1      2      0.109  284512.0 0.109  0

This is a terminal C-H bond of simple alkane. ( I am treating hydrogen with
mass = 8.0. it allows me to treat it as bond instead of lincs constraint. I
have also changed name of hydrogen which does not begin with H so that
gromacs distinguishes it from hydrogen and does not constrain it)

Similarly I turn off angle and dihedral constants to 0 in state B .

Is there anything which I need to include in the topology file (i.e. with
pairs etc..)?

I am doing this to check that my methodology is correct. I would expect
large positive DG value.

If I get this correctly then I would use it for the actual system where I
wish to see whether bond dissociation is favourable.

Initially I had used bond type 1 (generates exclusions ) and changed force
constant to 0 in state B. In that case the simulation did not crash. But
using Bond type 6 gives LINCS warnings.

Is it reasonable what I am doing?

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