On Jul 17, 2007, at 4:45 PM, 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 ("FreeEnergy 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 stateA 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?
Since a couple of years we automatically copy the A state parameters to the B state if the latter aren't specified.
So, there are really three options e.g. for an entry in the [ bonds ] section:
1. You only specify the bond atoms & type without any parameters (most common approach)
In this case, the A state parameters will be assigned based on the atomtypes in the A state, and the B state parameters likewise based on the B state atomtypes.
The interaction is perturbed.
2. You provide the A state parameters explicitly, but not any B state
parameters:
Since you've decided to override the automatic assignment your choice will be used in both the A and B states (i.e., the interaction will not be perturbed)
3. You provide both A and B state parameters explicitly:Your parameters will be assigned to each state, and the interaction is perturbed.
Cheers, Erik _______________________________________________ gmx-users mailing list [email protected] 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 [EMAIL PROTECTED]
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