Hi Vinicius,
This is very helpful to know! Thank you very much once again!
Have a great weekend,
Jason
ᐧ
On Fri, Apr 27, 2018 at 11:43 AM, Cruzeiro,Vinicius Wilian D <
vwcruzeiro.ufl.edu> wrote:
> Hello Jason,
>
>
> A Hamiltonian REMD dimension can be constructed by either changing a
> parameters inside the mdin file of each replica or by having each replica
> to use a different prmtop file. In either case, when a exchange attempt is
> successful, coordinates and velocities are swapped. As an addendum to my
> previous message: if the target temperatures in the two replicas that are
> being exchanged is different, then the velocities will also be rescaled to
> match the target temperature of the new replica.
>
>
> All the best,
>
>
> Vinícius Wilian D Cruzeiro
>
> PhD Candidate
> Department of Chemistry, Physical Chemistry Division
> University of Florida, United States
>
> Voice: +1(352)846-1633
>
> ________________________________
> From: Jason Ku Wang <jwang198.stanford.edu>
> Sent: Friday, April 27, 2018 1:54:23 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Multi-Dimensional REMD: rem.log shows exchanges along
> Hamiltonian dimension, but .mdout files do not
>
> Hi Vinícius,
>
> Thank you so much for the reply!
>
> I'm currently basing the Hamiltonian dimension on different parameters of
> accelerated MD. It makes sense to exchange coordinates and velocities when
> the Hamiltonian dimension is based off of varying topology files.
>
> But in the case of aMD-based Hamiltonian exchange, where only the input
> parameters differ (much like temperature-REMD), does this also hold?
>
> Thanks for the clarification - I just want to make sure I understand the
> implementation!
>
> Best,
> Jason
> ᐧ
>
> On Wed, Apr 25, 2018 at 6:29 PM, Cruzeiro,Vinicius Wilian D <
> vwcruzeiro.ufl.edu> wrote:
>
> > Hello Jason,
> >
> > In T-REMD, a given replica will have different target temperatures
> > throughout the simulation. Therefore, when you sort all replicas to
> filter
> > only the trajectories corresponding to a given temperature, you will get
> > chunks of data from many replicas (possibly from all if your exchange
> rate
> > is good and you run long enough).
> >
> > In H-REMD, a given replica exchanges coordinates and velocities when an
> > exchange attempt is accepted, but the replica index will remain the same
> > until the end of the simulation.
> >
> > Therefore, for your T,H-REMD simulation, the fact that the hamiltonian
> > index is not changing but the temperature index is actually is then
> > expected. If you are obtaining good exchange rates in the rem.log files,
> > then everything should be fine.
> >
> > I hope this helps,
> > Best,
> >
> >
> > Vinícius Wilian D Cruzeiro
> >
> > PhD Candidate
> > Department of Chemistry, Physical Chemistry Division
> > University of Florida, United States
> >
> > Voice: +1(352)846-1633<tel:+1(352)846-1633>
> >
> > On Apr 25, 2018, at 8:56 PM, Jason Ku Wang <jwang198.stanford.edu
> <mailto:
> > jwang198.stanford.edu>> wrote:
> >
> > Hi AMBER Community,
> >
> > I am currently running multi-dimensional REMD using a temperature and
> > Hamiltonian dimension (my Hamiltonian dimension is defined by varying
> > parameters for accelerated MD applied only to torsional potential
> > energies). To see if exchanges are occurring at a reasonable rate along
> > either dimension, I examine the rem.log files.
> >
> > Looking just at rem.log files, it appears that both temperature and
> > Hamiltonian dimensions are mixing well. In particular, we see *very clear
> > evidence* of exchanges occurring along the Hamiltonian dimension (note
> the
> > success and success rate columns):
> >
> > # Rep#, Neibr#, Temp0, PotE(x_1), PotE(x_2), left_fe, right_fe, Success,
> > Success rate (i,i+1)
> > # exchange 64 REMD group 45
> > 32 33 302.97-461315.96-460510.32 6.77 -6.77 T
> > 0.06
> > 10 30 302.97-460764.81-460769.68 6.46 -6.50 F
> > 0.06
> > 34 37 302.97-460835.06-460731.85 6.89 -6.72 T
> > 0.12
> > 1 10 302.97-460532.32-461501.22 -285.50 -6.32 F
> > 0.06
> > 17 16 302.97-461139.12-461040.58 6.59 -6.46 T
> > 0.06
> > 2 15 302.97-461393.48-461490.99 6.19 -6.38 T
> > 0.12
> > 26 20 302.97-461362.27-460938.11 6.70 -6.60 T
> > 0.12
> > ...
> >
> > However, when I attempt to examine *.mdout files*, I see no evidence of
> > exchange. If I look at the GROUP INDEX corresponding to the Hamiltonian
> > dimension, I see that it stays constant across every step. For example,
> for
> > any given replica, the first number corresponding to the Hamiltonian
> value
> > never changes, but the second number corresponding to temperature does
> > change. Yet, both Hamiltonian and temperature dimensions show reasonable
> > exchange rates in rem.log files.
> > ...
> > MULTI-D REMD. GROUP INDEXES: * 1* 2
> > ...
> >
> > I checked this systematically for all my replicas and my frequency of
> > printing is the same as my frequency of exchange.
> >
> > *Is this a potential bug? Why would the Hamiltonian group printed out in
> > the .mdout file remain unchanging even though the rem.log shows
> > Hamiltonians being exchanged?*
> >
> > Thanks so much for the help!
> > Jason
> >
> > --
> > Jason Wang
> > Stanford University, Class of 2018
> > jwang198.stanford.edu<mailto:jwang198.stanford.edu>
> > ᐧ
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> --
> Jason Wang
> Stanford University, Class of 2018
> jwang198.stanford.edu
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--
Jason Wang
Stanford University, Class of 2018
jwang198.stanford.edu
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Received on Fri Apr 27 2018 - 13:30:02 PDT
