Hi
You have to be more specific...
Did you just do one sim for Gly->Ala?
Are you sure, you did the simulations in a way, you can compare it to
exp. results? (think about doing the perturbation once in water and once
in vacuum or so)
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Soren Enemark wrote:
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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