[gmx-users] Free Energy Calculations in Gromacs
hanniballecter13 at gmail.com
Wed Apr 24 23:12:59 CEST 2013
Thank you Professor Shirts.
So now my protein itp file looks like this:
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
1 CT 1 ACE CH3 1 -0.190264 12.010000 CT_per
[ bonds ]
;ai aj func th0 kb th0B kbB
1 2 1 0.10900 284512.0 0.10900 113804.8
[ pairs ]
1 8 1
[ angles ]
;ai aj ak funct th0 kb th0B kbB
2 1 3 1 109.500 292.880 109.500 117.152
[ dihedrals ]
i j k l func th0 cth mult th0B cthB
2 1 5 6 9 180.0 2.86144 1 180.0 1.14458 1
Now, I have created 6 different lambda values and placed a
well-equilibrated structure and the same topology file (with values
corresp. to lambda=0 and lambda =1) within six directories. The .mdp files
contain the information (init-lambda-state=0,1,..) which lambda state is
Is my approach correct ?
Secondly, when I grompp followed by gmxdump -s *.tpr I find, that there is
no difference in hamiltonian between the two. So, does the scaling take
place during runtime?
Third, since in state B only the hamiltonian is rescaled (the perturbed
entries are defined in ffnonbonded.itp file) do I need to explicitly add
another section [ pairs_nb ]?
Again, I thank you for replying.
On Sat, Apr 20, 2013 at 5:52 PM, Michael Shirts <mrshirts at gmail.com> wrote:
> You have to change atom types. For example:
> [ atomtypes ]
> ;name bond_type mass charge ptype sigma epsilon
> h1 h1 0.0000 0.0000 A 2.47135e-01
> h1_pert h1 0.0000 0.0000 A 2.47135e-01 3.56888e-02
> ; perturbed
> The mass and charge can be zero, because they will be defined in the [
> atoms ] part
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass typeB
> chargeB MassB
> 1 h1 1 BLAH H1a 1 -0.089 1.008 h1_pert
> -0.030 1.008; perturbed
> On Sat, Apr 20, 2013 at 4:04 PM, HANNIBAL LECTER <
> hanniballecter13 at gmail.com
> > wrote:
> > Hi,
> > I am trying to perform expanded ensemble simulations between 2 states A
> > (lambda=0) and B (lambda =1) with 6 intermediate lambda values.
> > In state B the Hamiltonian is rescaled, such that the epsilons of the vdW
> > interactions, the charges, the bond, angle and dihedral constants are a
> > multiple of the similar terms of State A.
> > It's not quite clear to me (going through the archives of the gmx-users
> > mailing list how to perform these calculations. One way to do this, is to
> > use a single topology file in which the charges and the other terms are
> > specified for both states A and B. However, it is not clear as to how
> > should I scale the epsilons in the topology file. (My atoms are not
> > in state B. They are the same atoms with scaled epsilons.)
> > Secondly, since I have the topology files for states A and B, is there a
> > way I could perform the simulations (any particular way in grompp) where
> > both the topology files can be preprocessed designating the end states
> > using the mdp options, the simulations corresponding to the intermediate
> > lambda values performed??
> > --
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