Dear Amber Experts,
I used Amber 20 for running parallel GAMD simulations and I did not encounter any issue.
But when using the same simulation scripts on Amber 24, I have encountered these issues
* gamd-restart.dat file is not generated: Please see the gamd equilibration script.
* Randomly, few jobs are frozen (jobs are running but no outputs are generated): Please
see the error messages from SLURM system.
Will you please help me solving these issues.
*Equilibration Script:*
Equilibration NpT (93 ns): Distance restraint
&cntrl
!! [General minimization and dynamics parameters]
!! General flags describing the calculation & Energy minimization
imin = 0,
nmropt = 1,
!! Energy minimization
! maxcyc = 1,
! ncyc = 10,
! ntmin = 1,
! drms = 0.00010,
!! Nature and format of the input
ntx = 5,
irest = 1,
!! Nature and format of the output
ntpr = 5000,
! ntwr = nstlim,
! iwrap = 0,
! ntwx = 0,
! ntwv = 0,
! ntwf = 0,
! ntwe = 0,
! ntwprt = 0,
!! Restrained atoms
! ntr = 0,
! restraint_wt = 0.0,
! restraintmask = "",
!! Molecular dynamics
nstlim = 46500000,
nscm = 1000,
! t = 0.0,
dt = 0.002,
!! Temperature regulation
ntt = 3,
tempi = 310.0,
temp0 = 310.0,
gamma_ln = 5.0,
!! The “middle” scheme: can not be used with ntp > 0
! ischeme = 1,
! ithermostat = 1,
! therm_par = 5,
!! Pressure regulation
ntp = 1,
barostat = 1,
pres0 = 1.0,
taup = 1.0,
!! Surface tension regulation
! csurften = 0,
! gamma_ten = 0.0,
! ninterface = 2,
!! SHAKE bond length constraints
ntc = 2,
!! Potential function parameters
ntf = 2,
ntb = 2,
cut = 8.0,
!! Gaussian Accelerated Molecular Dynamics: It is not available in Sander
igamd = 3,
iE = 1,
ntcmdprep = 1000000,
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Received on Sat Jun 22 2024 - 20:30:02 PDT
