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

[Maik Goette]

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?
> 
> ------------------------------------------------------------------------
> 
> Alt i én. Få Yahoo! Mail <http://dk.mail.yahoo.com> med adressekartotek, 
> kalender og notesblok.
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php