[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

[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

[gmx-users] Free energy calculation: merge the topology of 2 molecules

Hi all, I'm trying to set-up a free energy calculation where a molecule has +2 charge in it's native state (state A) and no charge in the mutant (state B). Since the molecule has net +2 charge, I have to add counter-ions to neutralize the system in state A. But in order to transform it to state B

Re: [gmx-users] Free energy calculation: merge the topology of 2 molecules

> *Gesendet:* Donnerstag, 30. Mai 2013 um 20:48 Uhr > *Von:* "Dejun Lin" > *An:* gmx-users@gromacs.org > *Betreff:* [gmx-users] Free energy calculation: merge the topology of 2 > molecules > Hi all, > > I'm trying to set-up a free energy calculation where a

[gmx-users] Re: gmx 4.6.1, Expanded ensemble: weird balancing factors

I have a similar question here. Can anyone tell if the Wang-Landau algorithm in lambda space is robust in that it doesn't depend on the choice of the convergence factor (weight-equil-wl-delta), the flatness of the histogram (wl-ratio) and/or the frequency of trial move (nstexpanded), especially in

Re: [gmx-users] Re: gmx 4.6.1, Expanded ensemble: weird balancing factors

s new code in the hands of others it breaks in > ways that were not foreseen! > > On Tue, Jul 16, 2013 at 12:53 PM, Dejun Lin wrote: > > I have a similar question here. Can anyone tell if the Wang-Landau > algorithm > > in lambda space is robust in that it doesn't depend

[gmx-users] Re: gmx 4.6.1, Expanded ensemble: weird balancing factors

It seems to have something to do with the integrator/pressure-coupling. When I ran the tutorial on http://www.alchemistry.org/wiki/GROMACS_4.6_example:_Ethanol_solvation_with_expanded_ensemble, everything seems fine unless I switched to sd integrator instead of md-vv (and Pcoupl from MTTK to beren

Re: [gmx-users] Re: gmx 4.6.1, Expanded ensemble: weird balancing factors

The test I did was using gmx-4.6.3. I'm currently working on a membrane system, which requires semiisotropic pressure coupling. I know that MTTK in gmx-4.6.3 doesn't support semiiso yet so the only combination available for expanded ensemble is md-vv + v-rescale tcoupl + berendsen pcoupl, which I'm

[gmx-users] Replica exchange log file inconsistent with mdrun -replex

Hi all, I'm running a replica exchange simulation using gromacs 4.6.3 with the command line: mdrun_mpi -deffnm remd_ -multi 64 -replex 100 -nex 262144 I was expecting to get a log entry about the exchange every 100 steps but I only got one every 1000 steps. I wonder if the output was suppressed

[gmx-users] Re: Replica exchange log file inconsistent with mdrun -replex

OK. I found the problem is that when -replex is not a multiple of nstcalcenergy, it'll be converted to nstcalcenergy implicitly. -- View this message in context: http://gromacs.5086.x6.nabble.com/Replica-exchange-log-file-inconsistent-with-mdrun-replex-tp5010206p5010210.html Sent from the GROMA

[gmx-users] Expanded ensemble simulation died with fatal error: Something wrong in choosing new lambda state with a Gibbs move

Hi all, I'm running an expanded ensemble simulation using gromacs 4.6.3 and it crashed with the error: Fatal error: Something wrong in choosing new lambda state with a Gibbs move -- probably underflow in weight determination. Denominator is: 0 1.002384e+00 idEnumer

[gmx-users] restraint-lambdas for position restraints in hamiltonian exchange

Hi all, I went through the manual and couldn't find any definite answers to the following questions. First, I wonder if the reference positions of position restraints, not just the force constants, of different replicas are exchanged in hamiltonian exchange based on restraint-lambdas? For example

[gmx-users] Re: restraint-lambdas for position restraints in hamiltonian exchange

So I take it that in the position restraint case (not COM-pulling), where the reference positions are determined by the starting structure instead of a B-state topology, the reference positions won't be swapped ? 2013/8/3 Michael Shirts-2 [via GROMACS] < ml-node+s5086n5010324...@n6.nabble.com> >

[gmx-users] Re: restraint-lambdas for position restraints in hamiltonian exchange

alities to be > implemented. You can submit a request to redmine.gromacs.org so that > the request is archived. > > On Sat, Aug 3, 2013 at 6:12 PM, Dejun Lin <[hidden > email]<http://user/SendEmail.jtp?type=node&node=5010326&i=0>> > wrote: > > > So I take

[gmx-users] Re: restraint-lambdas for position restraints in hamiltonian exchange

a lot for your help! -Dejun 2013/8/7 Dejun Lin > Hi Micheal, > > Sorry for keep bugging you about this but I want to make sure I'm doing > what I think I'm doing :) > I did some test on the following setup. > > restraint-lambdas = 0.3 0.29 (essentiall