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From: Jason Ku Wang <jwang198.stanford.edu>

Date: Wed, 25 Apr 2018 17:44:45 -0700

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

Date: Wed, 25 Apr 2018 17:44:45 -0700

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 ᐧ _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Apr 25 2018 - 18:00:03 PDT

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