Dear Amber users,
I'm running Swarms-of-trajectories String Method in Amber 18, and these are a pair of example of my input files and cv files:
mdin.001:
&cntrl
imin=0, ntx=1, irest=0, ntxo=1, ntc=2, ntf=2, nstlim=10000,
ntt=3, gamma_ln=2.0, temp0=300.0, ntpr=10, ntwr=10, ntwx=10,
dt=0.002, ig=-1, ntb=1,ntr=0, cut=10.0, ioutfm=1, iwrap=1,infe=1,
/
&stsm
image = 1
repeats = 20
equilibration = 980
release = 20
smoothing = 0.06
report_centers = 'ALL'
output_file = 'stsm.001.txt'
output_freq = 10
cv_file = 'cv.1'
/
cv.1:
&colvar
cv_type = 'TORSION'
cv_ni = 4, cv_i = 5653, 5639, 5620, 5551
anchor_position = 0.5235
anchor_strength = 20.0
/
&colvar
cv_type = 'TORSION'
cv_ni = 4, cv_i = 5541, 5649, 5653, 3386
anchor_position = 1.5705
anchor_strength = 20.0
/
The command is: nohup /software/amber18/bin/pmemd.cuda -O -i mdin.001 -p new_mono.prmtop -c inpcrd.001 -o test1.out -x test1.nc -r test1.restrt -inf test1.info & . And it came out the following error:
Program received signal SIGFPE: Floating-point exception - erroneous arithmetic operation.
Backtrace for this error:
#0 0x7FCB8B688E08
#1 0x7FCB8B687F90
#2 0x7FCB8AA374AF
#3 0x6AE5A1 in __nfe_stsm_mod_MOD_on_pmemd_init
#4 0x677A84 in __nfe_setup_mod_MOD_on_pmemd_init
#5 0x4B56DB in MAIN__ at pmemd.F90:?
When I set infe to 0 to turn stsm down, it works well. I couldn't figure out what the problem is. Have you met similar situations before? What should I do about this?
Thank you!
Best,
Yao Li
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Received on Sat Mar 16 2019 - 07:00:02 PDT
