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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Received on Wed Apr 25 2018 - 18:30:03 PDT
