Dear Gromacsers,
I have been doing free energy perturbations Gly->Ala in one strand of
collagene.
Now, the problem is that I have later closely reread the section 5.6.4 ("Free
Energy Calculations") p. 105 in which it says:
"Bonded interactions between atoms that are not perturbed do not need B
parameter specifications ..".
My questions are:
1. Does this mean that bonded interactions between atoms that ARE perturbed
DO need B parameter specifications? Even if they are the same in state
A and B?
2. What about the other topology parameters (angles, dihedrals etc), do they
need to be specified too?
3. What happens if I have not specified these specifications?
The relevant parts of the topology file which I use are:
[ atoms ]
....
87 N 13 ALA N 49 -0.28 14.0067 ; qtot
0.72
88 H 13 ALA H 49 0.28 1.008 ; qtot 1
89 CH2 13 ALA CA 50 0 14.027 CH1 0.0
3.019 ; qtot 1
90 DUM 13 ALA CB 50 0 15.035 CH3 0.0
15.035 ; qtot 1
91 C 13 ALA C 51 0.38 12.011 ; qtot
1.38
92 O 13 ALA O 51 -0.38 15.9994 ; qtot 1
...
[ bonds ]
...
87 89 2 gb_20
89 90 2 gb_26
89 91 2 gb_26
...
[ angles ]
....
85 87 89 2 ga_30
88 87 89 2 ga_17
87 89 90 2 ga_12
87 89 91 2 ga_12
90 89 91 2 ga_12
89 91 92 2 ga_29
89 91 93 2 ga_18
....
And so on, ie, no B specifications have been done except for the atoms!
Best regards, and thank you in anticipation,
Soren
Ps. One (non-gromacs -sorry) question, given that the above is not wrong:
For the pertubation Gly->Ala I have get a deltaG of 0.8 kcal/mol. Looking
through literature, this does not seem all wrong, say if the pertubation took
place in an alpha-helix. On the other hand, it is close to the thermal energy
(~kT), and a previous article doing the exact same perturbation arrives at a
deltaG around 8.6 kcal/mol. Could anyone comment on that?
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