Automatic Parameter Tuning for REMD, REUS, REST

Strategy

In REMD simulations, we need to define “good” parameter set to achieve random walk in parameter space to perform calculations efficiently. In case of T-REMD, there is a good way to determine the parameter set. But in REUS or REST, no general ways are available so far. This is one of the most annoying points in those calculations. To solve this problem, an intuitive parameter tuning mechanism is implemented in GENESIS (both of ATDYN and SPDYN).

Assume we have n replica parameters (such as temperatures) \(V_{0}, V_{1}, V_{2}, \cdot\cdot\cdot, V_{n}\). In this setup, we cave n-1 deltas between adjacent values \(X_{0,1}, X_{1,2}, X_{2,3}, \cdot\cdot\cdot, X_{n-1,n}\). Here we try to change these “X” values to get a good set of parameters, while one of terminal values is fixed.

Deviation of the exchange probability between replicas i and j, \(\Delta p_{ij}\), from the target exchange probability, \(p_{\rm tgt}\), can be written as:

\(\displaystyle{\Delta p_{ij} = p_{ij} – p_{{\rm tgt}} – {\rm sign}(p_{ij} – p_{tgt}) \cdot {\rm max}({\rm abs}(p_{ij} – p_{{\rm tgt}}),p_{{\rm mgn}})}\),

where \(p_{ij}\) is the exchange probability between replicas i and j, and margin is also considered. If the exchange probability is within the range of \(p_{\rm tgt}-p_{\rm mgn} < p_{ij} < p_{\rm tgt}+p_{\rm mgn}\), the exchange works fine. This formula says that if the exchange prob. is larger (smaller) than the target value, \(\Delta p_{ij}\) is large (small).

\(X_{0:1}, X_{1:2}, X_{2:3}, \cdot\cdot\cdot, X_{n-1:n}\) will be updated according to the following equation:

\(\displaystyle{\Delta X_{i:j} = \Delta p_{ij} \cdot 100 \cdot v_g}\),

where \(v_g\) is the grid size in parameter space. If the exchange probability deviation is large, large change will happen in the parameter values. Parameter set is recalculated from the fixed terminal value and the Xs upon update. Repeating update according to this scheme, the exchange probabilities will get close to the target value.

List of Parameters in GENESIS

These parameters are available in [REMD] section. In the following list, “N” should be replaced to an integer number like other params.

param_tuningN = YES / NO (default: NO)

This parameter defines whether the parameter tuning is enabled.

tgt_exc_probN = Real (default: 0.25)

This parameter defines target exchange probability. The valid value range is 0.0-1.0. (\(p_{\rm tgt}\))

mgn_exc_probN = Real (default: 0.05)

This parameter defines the margin for the target exchange probability. Parameters would not change if the following condition is satisfied: tgt_exc_prob – mgn_exc_prob < exchange probability < tgt_exc_prob + mgn_exc_prob. (\(p_{\rm mgn}\))

trial_freqN = Integer (default: 48)

Number of trials used for single update of parameter set. In the real calculations, update of parameter set takes place after (trial_freqN * 2) exchange trials. This is because there are two exchange patterns in GENESIS.

eq_cycleN = Integer (default: 2)

Number of equilibration cycles after the parameter set update. As trial_freqN above, (eq_cycleN * 2) exchange trials will be ignored.

param_gridN = Real (default: 0.1)

Grid of parameter space. (\(v_g\))

max_param_shiftN = Real (default: 20.0)

Maximum parameter shift in a single update. If you specify large values, this value is virtually ignored.

fix_terminalN = BOTTOM / TOP (default: BOTTOM)

Determines parameter value to be fixed. In case of BOTTOM, the first value in the parameter list is fixed. On the other hand, the last value in the parameter list is fixed if TOP is specified.

Samples

  • exchange_period must not be 0 if you perform parameter tuning.
  • exchange_period should be small for the first tuning stage.
  • updated parameters are not saved in restart files. You should write new values in your next input file.
  • if you wanna do fine tuning, increase exchange_period and trial_freqN values.
T-REMD example

(Parameter update takes place every 5,000 steps.)

[REMD]
dimension        = 1
exchange_period  = 50
iseed            = 3141592

type1            = TEMPERATURE
nreplica1        = 4
parameters1      = 300 301 301.7 303.2

param_tuning1    = YES
tgt_exc_prob1    = 0.25
mgn_exc_prob1    = 0.05
trial_freq1      = 48
eq_cycle1        = 2
param_grid1      = 0.1
max_param_shift1 = 20.0 # virtually ignored
fix_terminal1    = BOTTOM

Sample log message (extracted from the main log file):

REMD> New parameter set: 300.00000 303.00000 303.10000 311.60000
REMD> New parameter set: 300.00000 301.00000 308.10000 314.60000
REUS example

(only reference values will change upon update.)

[REMD]
dimension        = 1
exchange_period  = 50
iseed            = 3141592

type1            = RESTRAINT
nreplica1        = 4
cyclic_params1   = NO
rest_function1   = 1

param_tuning1    = YES
tgt_exc_prob1    = 0.25
mgn_exc_prob1    = 0.05
trial_freq1      = 48
eq_cycle1        = 2
param_grid1      = 0.01
max_param_shift1 = 0.2
fix_terminal1    = BOTTOM

[SELECTION]
group1           = an:H62 and resno: 9
group2           = an:H62 and resno: 10

[RESTRAINTS]
nfunctions       = 1
function1        = DIST          # restraint function type
constant1        = 15 15 15 15   # force constants
reference1       = 4 4.1 4.3 4.5 # references
select_index1    = 1 2           # restrained groups

Sample log message (extracted from the main log file):

REMD> New parameter set: 4.00000 4.30000 4.31000 4.32000
REMD> New parameter set: 4.00000 4.50000 4.71000 4.92000
REST example

(almost the same as T-REMD)

[REMD]
dimension        = 1
exchange_period  = 50
iseed            = 3141592

type1            = REST
nreplica1        = 4
parameters1      = 300 301 301.7 303.2
select_index1    = 1

param_tuning1    = YES
tgt_exc_prob1    = 0.25
mgn_exc_prob1    = 0.05
trial_freq1      = 48
eq_cycle1        = 2
param_grid1      = 0.1
max_param_shift1 = 20.0
fix_terminal1    = BOTTOM

[SELECTION]
group1           = ai:1-638

Sample log message (extracted from the main log file):

REMD> New parameter set: 300.00000 303.00000 310.70000 319.20000
REMD> New parameter set: 300.00000 305.00000 314.70000 330.20000