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Bug #3304

Failure in Log Output for Expanded Ensemble Weights using Simulated Tempering in GROMACS 2019.5

Added by Daniel Kozuch about 1 month ago.

Status:
New
Priority:
Normal
Category:
Logging
Target version:
Affected version - extra info:
with GPU
Affected version:
Difficulty:
uncategorized
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Description

When using simulated tempering with metropolis transition the log output for the lambda weights is only 0, inf, or -nan (see log output example below). The mdp settings are shown below the log output. I can attach a .gro and .top file if need be, but I think this is not system dependent. I think there is also an error in the documentation, "lmc-mc-move" should be "lmc-move".

Log output:
--------------------------------------------

MC-lambda information
N Temp.(K) Count G(in kT) dG(in kT)
1 300.000 0 0.00000 0.00000
2 301.000 0 0.00000 0.00000
3 302.000 3 0.00000 inf
4 303.000 6 inf -nan
5 304.000 6 inf -nan <<
6 305.000 4 inf -nan
7 306.000 1 -nan -nan
8 307.000 0 -nan -nan
9 308.000 0 -nan -nan
10 309.000 0 -nan -nan
11 310.000 0 -nan 0.00000

MDP Settings:
----------------------------------------------------

integrator = md-vv
dt = 0.002
nstcomm = 100

nstlog = 500
nstcalcenergy = 100
nstenergy = 500
nstxtcout = 500
nstvout = 0
xtc-precision = 1000

cutoff-scheme = Verlet
nstlist = 10
ns-type = Grid
pbc = xyz
periodic-molecules = no
rlist = 1

coulombtype = PME
coulomb-modifier = Potential-shift-Verlet
rcoulomb = 1
vdw-type = Cut-off
vdw-modifier = Potential-shift-Verlet
rvdw = 1
DispCorr = EnerPres
optimize-fft = yes

tcoupl = v-rescale
nsttcouple = -1
nh-chain-length = 10
tc-grps = Protein Non-Protein
tau-t = 0.2 0.2
ref-t = 300 300
pcoupl = Berendsen
pcoupltype = Isotropic
nstpcouple = -1
tau-p = 2
compressibility = 0.000045
ref-p = 1 1 1 0 0 0

gen-vel = yes
gen-temp = 300
gen-seed = -1

constraints = h-bonds
constraint-algorithm = LINCS
continuation = no

; EXPANDED ENSEMBLE
simulated-tempering = yes
nstexpanded = 100
sim-temp-low = 300
sim-temp-high = 310
simulated-tempering-scaling = linear
lmc-stats = metropolis-transition
lmc-move = metropolis
temperature-lambdas = 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0
init-lambda-state = 3
lmc-weights-equil = no
nstdhdl = 100

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