[gmx-users] free energy perturbations and B-parameter specifications

[Soren Enemark]

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?

 		
---------------------------------

Alt i én. Få Yahoo! Mail med adressekartotek, kalender og notesblok. 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070717/c86dcb53/attachment.html>