Hi Michael,
Do the codes now support walking in multidimensional parameter space? i.e.,
a state is defined by a set of lambda parameters {l1,l2,l3,...,ln} and a MC
move is attempted along one of the parameter, which is randomly picked.
Thanks,
Dejun
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Hi, Dejun-
Right now, the vector of lambda parameters is simply vdw, coul, bonded,
restraint, temperature. You can't have, say, 2 different coul vectors or
two different restraint vectors for different restraints. But you can
change any of these components.
You define the vector manually by
Hi Micheal,
Just to make sure I understand you correctly -- I can have 1 type of
restraint, e.g., a harmonic potential between 2 groups defined by (k1, d1)
where k1 is force constant and d1 is the equilibrium position. But I can't
have 2 or more types of restraints like (k1,d1,k2,d2,...,kn,dn).
. Will try to play around with this later
today.
Best,
Joakim
Date: Thu, 7 Mar 2013 08:55:31 -0500
From: Michael Shirts mrshi...@gmail.com
Subject: Re: [gmx-users] Hamiltonian replica exchange umbrella
sampling with gmx 4.6
To: Discussion list for GROMACS users gmx-users@gromacs.org
Hi
Dear Michael,
Thank you for your reply.
Yes, it is relatively clear now. Will try to play around with this later today.
Best,
Joakim
Date: Thu, 7 Mar 2013 08:55:31 -0500
From: Michael Shirts mrshi...@gmail.com
Subject: Re: [gmx-users] Hamiltonian replica exchange umbrella
sampling
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