Dear Amber Users,
I successfully conducted a LiGaMD3 simulation on my system using Amber24. However,
when I ran the same system with the same input parameters in Amber26, the simulation
consistently crashed immediately after the ntcmd steps.
The input file is attached for reference.
The error message reported in slurm.out is:
Failed: an illegal memory access was encountered
The mdout file shows that the conventional MD stage completes successfully, but the crash
occurs immediately after the message indicating that the boost potential is being applied:
GaMD: Apply boost potential after finishing conventional MD; igamd = 28
Any suggestions or insights into the cause of this issue would be greatly appreciated.
Thank you for your time and assistance.
the last 100 lines in mdout:
===============================================================================
NSTEP = 2490000 TIME(PS) = 11980.000 TEMP(K) = 309.82 PRESS = -22.4 Etot = -282754.4703
EKtot = 55527.9051 EPtot = -338282.3754 BOND = 1686.4132 ANGLE = 4900.5460 DIHED =
3078.6209 UB = 0.0000 IMP = 0.0000 CMAP = 458.5482 1-4 NB = 1978.8007 1-4 EEL = 26909.8460
VDWAALS = 39703.2927 EELEC = -417002.7780 EHBOND = 0.0000 RESTRAINT = 4.3351
EAMBER (non-restraint) = -338286.7104 EKCMT = 24555.6027 VIRIAL = 24978.6512 VOLUME =
873386.8069 Density = 1.0251 ------------------------------------------------------------------------------ NMR
restraints: Bond = 4.335 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 2495000 TIME(PS) = 11990.000 TEMP(K) = 309.63 PRESS = 108.6 Etot = -283096.8158
EKtot = 55493.7313 EPtot = -338590.5471 BOND = 1706.8708 ANGLE = 4822.0121 DIHED =
3047.9928 UB = 0.0000 IMP = 0.0000 CMAP = 444.6204 1-4 NB = 1989.6048 1-4 EEL = 26959.0056
VDWAALS = 40215.2069 EELEC = -417779.9323 EHBOND = 0.0000 RESTRAINT = 4.0717
EAMBER (non-restraint) = -338594.6188 EKCMT = 24724.5769 VIRIAL = 22677.5464 VOLUME =
872710.3674 Density = 1.0259 ------------------------------------------------------------------------------ NMR
restraints: Bond = 4.072 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 2500000 TIME(PS) = 12000.000 TEMP(K) = 310.53 PRESS = 96.0 Etot = -282651.2339
EKtot = 55655.6808 EPtot = -338306.9147 BOND = 1719.5026 ANGLE = 4849.1341 DIHED =
3114.1974 UB = 0.0000 IMP = 0.0000 CMAP = 432.2616 1-4 NB = 1990.4003 1-4 EEL = 26922.8517
VDWAALS = 40254.9493 EELEC = -417590.6281 EHBOND = 0.0000 RESTRAINT = 0.4163
EAMBER (non-restraint) = -338307.3310 EKCMT = 24516.2390 VIRIAL = 22709.9486 VOLUME =
871574.4285 Density = 1.0272 GAMD = 0.0000 GAMD_environment -347989.7489
------------------------------------------------------------------------------ NMR restraints: Bond = 0.416 Angle =
0.000 Torsion = 0.000
===============================================================================
|
===============================================================================
A V E R A G E S O V E R 500000 S T E P S NSTEP = 2500000 TIME(PS) = 12000.000 TEMP(K) =
310.00 PRESS = 0.9 Etot = -282878.7647 EKtot = 55560.1420 EPtot = -338438.9067 BOND =
1719.4400 ANGLE = 4815.4978 DIHED = 3106.4917 UB = 0.0000 IMP = 0.0000 CMAP = 444.2274
1-4 NB = 1990.3545 1-4 EEL = 26959.9902 VDWAALS = 40142.4359 EELEC = -417620.6653
EHBOND = 0.0000 RESTRAINT = 3.3211 EAMBER (non-restraint) = -338442.2277 EKCMT =
24531.7023 VIRIAL = 24513.9521 VOLUME = 872272.4354 Density = 1.0264 GAMD = 0.0000
GAMD_environment -348080.3362 ------------------------------------------------------------------------------ R M S F
L U C T U A T I O N S NSTEP = 2500000 TIME(PS) = 12000.000 TEMP(K) = 1.03 PRESS = 94.9 Etot
= 333.4687 EKtot = 184.7237 EPtot = 274.6963 BOND = 35.4194 ANGLE = 53.1438 DIHED =
27.8990 UB = 0.0000 IMP = 0.0000 CMAP = 10.8890 1-4 NB = 19.2276 1-4 EEL = 53.6927
VDWAALS = 270.3082 EELEC = 436.5871 EHBOND = 0.0000 RESTRAINT = 1.7992 EAMBER
(non-restraint) = 272.8971 EKCMT = 123.5770 VIRIAL = 1789.4089 VOLUME = 885.3624 Density
= 0.0010 GAMD = 0.0000 GAMD_environment 267.7646
------------------------------------------------------------------------------ |
===============================================================================
Energy statistics: step,VmaxP,VminP,VavgP,sigmaVP = 2500000 0.0000 0.0000 0.0000 0.0000
Energy statistics: step,VmaxD,VminD,VavgD,sigmaVD = 2500000 -346812.4721 -349355.4634
-348080.3362 267.7646 Energy statistics: step,VmaxB,VminB,VavgB,sigmaVB = 2500000
9972.0142 9337.0657 9641.4295 68.5847 | GaMD WARNING: switch iE = 2 to iE = 1 (i.e., E =
Vmax) | GaMD WARNING: k0" = NaN | GaMD WARNING: k0 is thus set to 1.0000 | GaMD
updated parameters: step,VmaxP,VminP,VavgP,sigmaVP,k0P,kP,EthreshP = 2500000 0.0000
0.0000 0.0000 0.0000 1.0000 Infinity 0.0000 | GaMD updated parameters:
step,VmaxD,VminD,VavgD,sigmaVD,k0D,kD,EthreshD = 2500000 -346812.4721 -349355.4634
-348080.3362 267.7646 0.0449 0.0000 -346812.4721 | GaMD updated parameters:
step,VmaxB,VminB,VavgB,sigmaVB,k0B,kB,EthreshB = 2500000 9972.0142 9337.0657 9641.4295
68.5847 0.1680 0.0003 9972.0142 | GaMD: Apply boost potential after finishing conventional
MD; igamd = 28
Kind regards,
--------------------
Morad Mustafa
Associate Professor of Computational Biophysical Chemistry
Equilibration NpT (93 ns): Distance restraint
&cntrl
!! [General minimization and dynamics parameters]
!! General flags describing the calculation & Energy minimization
imin = 0, ! Run molecular dynamics without any minimization.
nmropt = 1, ! NMR restraints and weight changes will be read.
!! Energy minimization
! maxcyc = 1, ! The maximum number of cycles of minimization; default.
! ncyc = 10, ! After NCYC cycles, switch from steepest descent to conjugate gradient; default.
! ntmin = 1, ! Flag for the method of minimization; default: steepest descent then conjugate gradient.
! drms = 0.00010, ! The convergence criterion for the energy derivative [kcal/(mole*A)]; default.
!! Nature and format of the input
ntx = 5, ! Coordinates and velocities will be read. Box information will be read if ntb > 0.
irest = 1, ! Flag to restart a simulation.
!! Nature and format of the output
ntpr = 5000, ! Every ntpr steps, print energy information to files mdout and mdinfo.
! ntwr = nstlim, ! Every ntwr steps during dynamics, write the restrt file; default.
! iwrap = 0, ! Wrap the coordinates written to the restart and trajectory files into a primary box; default, no wrap.
! ntwx = 5000, ! Every ntwx steps, write the coordinates to the mdcrd file.
! ntwv = 0, ! Every ntwv steps, write the velocities to the mdvel file; default
! ntwf = 0, ! Every ntwf steps, write the forces to the mdfrc file; default.
ntwe = 1000, ! Every ntwe steps, write the energies and temperatures to file "mden.
! ntwprt = 0, ! Number of atoms to include in trajectory files; default: include all atoms.
!! Restrained atoms
! ntr = 0, ! Flag for restraining specified atoms in Cartesian space using a harmonic potential; default.
! restraint_wt = 0.0, ! The weight for the positional restraints [in kcal/(mol.A^2)].
! restraintmask = "", ! String that specifies the restrained atoms.
!! Molecular dynamics
nstlim = 46500000, ! nteb + ntcmd. Number of MD-steps to be performed.
nscm = 1000, ! Every nscm steps, remove the translational center-of-mass motion; default.
! t = 0.0, ! The time at the start (psec); default.
dt = 0.002, ! The time step (psec) [Recommended is 0.002 if SHAKE is used].
!! Temperature regulation
ntt = 3, ! Switch for temperature scaling. Use Langevin dynamics.
tempi = 310.0, ! Initial temperature.
temp0 = 310.0, ! Reference temperature at which the system is to be kept.
gamma_ln = 5.0, ! The collision frequency in ps^−1.
!! The “middle” scheme: can not be used with ntp > 0
! ischeme = 1, ! Flag for choosing an integration scheme for molecular dynamics; “middle” scheme based on the leapfrog algorithm.
! ithermostat = 1, ! Flag for different thermostats when the “middle” scheme is employed, Langevin dynamics.
! therm_par = 5, ! The parameter used in a thermostatting method in the unit of ps^−1.
!! Pressure regulation
ntp = 1, ! Flag for constant pressure dynamics; isotropic position scaling.
barostat = 1, ! Flag used to control which barostat to use in order to control the pressure; default, Berendsen barostat.
pres0 = 1.0, ! Reference pressure (in units of bars, where 1 bar ≈ 0.987 atm); default.
taup = 1.0, ! Pressure relaxation time (in ps); default.
!! Surface tension regulation
! csurften = 0, ! Flag for constant surface tension dynamics; default.
! gamma_ten = 0.0, ! Surface tension value in units of dyne/cm. Default value is 0.0 dyne/cm.
! ninterface = 2, ! Number of interfaces in the periodic box; default.
!! SHAKE bond length constraints
ntc = 2, ! Flag for SHAKE to perform bond length constraints.
!! Potential function parameters
ntf = 1, ! Force evaluation; complete interaction is calculated (default).
ntb = 2, ! Flag for periodic boundaries conditions; default, if ntp > 0, constant pressure.
cut = 8.0, ! This is used to specify the nonbonded cutoff, in Angstroms.
!! Ligand Gaussian Accelerated Molecular Dynamics 3 (LiGaMD3): It is available in only the serial GPU version of pmemd (pmemd.cuda)
igamd = 28, ! Flag to apply boost potential
iE = 1, ! Flag to set the threshold energy E. (default) set the threshold energy to the lower bound E = V max
iEP = 2, ! Flag to overwrite iE and set the threshold energy E for applying the first boost potential in dual-boost schemes
iED = 1, ! Flag to overwrite iE and set the threshold energy E for applying the second boost potential in dual-boost schemes
iEB = 1, ! Flag to overwrite iE and set the threshold energy E for applying the third boost potential in the triple-boost schemes; LiGaMD3
ntcmdprep = 1000000, ! 2 * ntave. The number of preparation conventional molecular dynamics steps.
ntcmd = 2500000, ! 5 * ntave. The number of initial conventional molecular dynamics simulation steps.
ntebprep = 1000000, ! 2 * ntave. The number of preparation biasing molecular dynamics simulation steps.
nteb = 44000000, ! tens of ns. The number of biasing molecular dynamics simulation steps.
ntave = 500000, ! 4 * system atoms. The number of simulation steps used to calculate the average and standard deviation of potential energies.
irest_gamd = 0, ! Flag to restart GaMD simulation; default: new simulation.
sigma0P = 6.0, ! The upper limit of the standard deviation of the first potential boost that allows for accurate reweighting. The default is 6.0 (unit: kcal/mol).
sigma0D = 6.0, ! The upper limit of the standard deviation of the second potential boost that allows for accurate reweighting in dual-boost simulations The default is 6.0 (unit: kcal/mol).
sigma0B = 6.0, ! The upper limit of the standard deviation of the third potential boost that allows for accurate reweighting in triple-boost simulations (e.g., igamd = 28). The default is 6.0 (unit: kcal/mol).
timask1 = '(:574)', ! Specifies atoms of the first (bound) ligand, peptide or the first protein in ambmask format.
scmask1 = '(:574)', ! Specifies atoms of the first (bound) ligand that will be described using soft core in ambmask format in LiGaMD.
timask2 = '', !
scmask2 = '', !
bgpro2atm = 1, ! Start atomic number of the protein region in LiGaMD3
edpro2atm = 573, ! End atomic number of the protein region in LiGaMD3
nlig = 1, ! The total number of ligand molecules in the system. The default is 0
icfe = 1, ! The basic flag for free energy calculations. The default value of 0 skips such calculations. Setting this flag to 1 turns them on.
ifsc = 1, ! Flag for soft core potentials. 0 SC potentials are not used (default)
gti_cpu_output = 0, ! Controls whether per-residue or per-group energy decompositions are written for group-based TI. No per-group output (default).
! gti_add_sc = 1, ! Flag to control the non-bonded interactions between the common and softcore regions, and within the softcore regions. Include softcore atoms in the energy decomposition groups. default 1.
/
!! Particle Mesh Ewald
&ewald
order = 4, ! The order of the B-spline interpolation; default.
ew_type = 0, ! Turns on the particle mesh ewald (PME) method; default.
skinnb = 2.0, ! Width of the nonbonded skin in Angstroms; default.
!! Polarizable potentials: The following parameters are relevant, when ipol is set to 1 and dt = 0.001
/
!! Dipole Printing: Activate this when group input is not in use for something else (i.e. restraints)
! &dipoles
! /
!! Varying conditions
&wt
TYPE = 'END',
/
DISANG=distance.rst
LISTIN=POUT
LISTOUT=POUT
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Received on Tue Jun 30 2026 - 02:30:02 PDT
