[gmx-users] Re: Hamiltonian replica exchange umbrella sampling with gmx 4.6

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). Is

Re: [gmx-users] Re: Hamiltonian replica exchange umbrella sampling with gmx 4.6

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 wri

[gmx-users] Re: Hamiltonian replica exchange umbrella sampling with gmx 4.6

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 -- View this message in context: http://gro

Re: [gmx-users] Re: Hamiltonian replica exchange umbrella sampling with gmx 4.6

Great -- if it doesn't seem to be working the way it should after some playing around, then submit it as a redmine issue, and I'll take a look. On Fri, Mar 8, 2013 at 2:51 AM, Joakim Jämbeck wrote: > Dear Michael, > > Thank you for your reply. > > Yes, it is relatively clear now. Will try to play

[gmx-users] Re: Hamiltonian replica exchange umbrella sampling with gmx 4.6

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 > Subject: Re: [gmx-users] Hamiltonian replica exchange umbrella > sampling with gmx 4.6 >