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 ("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?
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
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