Lei,
I am also confused about the details of dgdl (or dHdl) calculation in
GROMACS. For example, if the lambda is fixed at certain value, how did the
program determine dHdl?
See below.
My initial understanding was kind of similiar to that of Mauricio that dHdl
equals the difference in total
Dear David and Mauricio,
I am also confused about the details of dgdl (or dHdl) calculation in GROMACS. For example, if the lambda is fixed at certain value, how did the program determine dHdl?
My initial understanding was kind of similiar to that of Mauricio that dHdl equals the difference in to
Mauricio,
I'm somewhat confused by your question and notation. However, I think
the basic answer is something like this: In molecular dynamics, you
know the Hamiltonian from which you are sampling; call it H(x,p, l),
where x denotes all of the positions, p the momentums, and l lambda.
This, of co
Dear experts
I am doing FEP (thermodynamic integration method) simulations.
I have a questions about calculation in GROMACS.
Take in mind equation 3.77 from the GROMACS 3.3 manual.
There, dA/dl is calculated as
dA/dl = SS{ (dH/dl) exp()dp dq } / SS{ exp()dp dq = NVT;l }
where SS are doble integ
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