Dear Amber Users,
Please, kindly help me. I am trying to do Adaptively Biased MD Simulations
of type "distance" using "FLOODING". Although the simulation runs, but it
appears to me that it is not doing Adaptively Biased MD with flooding at
all because I do not see any such information in the amber output file at
all, and 'abmd.txt' and 'umbrella.nc' files were never written to hard
drive.
Since I did not get any error message, it is very hard for me to know what
exactly is wrong. And I think something is not okay because 'abmd.txt' and
'umbrella.nc' files were never written to hard drive.
I have tried AMBER16's pmemd, and pmemd.cuda as well as AMBER14's pmemd,
pmemd.cuda. I got similar behavior in all the cases.
Please, kindly guide me. The content of my input file is shown below. I
also include a section of my output file that contains information about
"control data for the run."
With regards
Emmanuel Salawu
emmanuel.salawu.gmail.com
++++++++++++++++++START_OF_AMBER_INPUT+++++++++++++++++++++
Type of Simulation Being Done, Equilibration 2,
&cntrl
ntxo=2, IOUTFM=1, !NetCDF Binary Format.
imin=0, !MD Simulation
irest=1, !Restart the Simulation, reading Coordinates and Velocities from
a p
ig=-1, !Pseudo-random number seed is changed with every run.
ntx=5, !Coordinates and Velocities will be read; a formatted (ASCII)
coordina
nstlim=750000, !Number of MD-steps to be performed. Default 1.
dt=0.00200, !The time step (psec). Recommended MAXIMUM is .002 if SHAKE
is us
cut=10.00000, !Cut Off Distance for Non-Bounded Interactions
!skinnb=4.00000, !Width of the nonbonded "skin". The direct sum nonbonded
lis
ntb=2, !Constant Pressure (default when ntp > 0)
igb=0, !No Generalized Born
ntp=1, !MD with isotropic position scaling
ntf=2, !Bond Interactions involving H-atoms omitted
ntc=2, !Bonds involving Hydrogen are Constrained
ntpr=1000, !Every 1000 steps, energy information will be printed in
human-rea
ntwx=10000, !Every 10000 steps, the coordinates will be written to the
mdcrd
ntwr=10000, !Every 10000 steps during dynamics, the restart file will be
writ
ntt=3, !Use Langevin Dynamics with the Collision Frequency GAMA given by
gamm
gamma_ln=2.00000, !Collision Frequency, ps ^ (-1)
temp0=350.00000, !Reference temperature at which the system is to be kept
tempi=350.00000, !Initial Temperature
pres0=1.01300, !Reference Pressure (in units of bars, where 1 bar = 0.987
atm
!saltcon=0.2, !Salt concentration
/
ncsu_abmd
mode = FLOODING
monitor_file = 'abmd.txt'
monitor_freq = 100
umbrella_file = 'umbrella.nc'
timescale = 1000.0 ! in ps
variable
type = DISTANCE
i = (209, 242)
min = 3.3 max = 3.7 ! min is not needed for DISTANCE
resolution = 0.5 ! required for mode = FLOODING
end variable
variable
type = DISTANCE
i = (213, 247)
min = 7.6 max = 8.0 ! min is not needed for DISTANCE
resolution = 0.5 ! required for mode = FLOODING
end variable
variable
type = DISTANCE
i = (780, 813)
min = 3.3 max = 3.7 ! min is not needed for DISTANCE
resolution = 0.5 ! required for mode = FLOODING
end variable
variable
type = DISTANCE
i = (784, 818)
min = 7.6 max = 8.0 ! min is not needed for DISTANCE
resolution = 0.5 ! required for mode = FLOODING
end variable
end ncsu_abmd
++++++++++++++++++END_OF_AMBER_INPUT+++++++++++++++++++++
+++++++++++++START_PART_OF_MY_OUTPUT+++++++++++++++++
2. CONTROL DATA FOR THE RUN
---------------------------------------------------------------------
default_name
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 5, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 2, ntpr = 1000, ntrx = 1, ntwr =
10000
iwrap = 0, ntwx = 10000, ntwv = 0, ntwe =
0
ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat=
0
Potential function:
ntf = 2, ntb = 2, igb = 0, nsnb =
25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 750000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = -1.00000
Langevin dynamics temperature regulation:
ig = 955799
temp0 = 350.00000, tempi = 350.00000, gamma_ln= 2.00000
Pressure regulation:
ntp = 1
pres0 = 1.01300, comp = 44.60000, taup = 1.00000
SHAKE:
ntc = 2, jfastw = 0
tol = 0.00001
| Intermolecular bonds treatment:
| no_intermolecular_bonds = 1
| Energy averages sample interval:
| ene_avg_sampling = 1000
Ewald parameters:
verbose = 0, ew_type = 0, nbflag = 1, use_pme =
1
vdwmeth = 1, eedmeth = 1, netfrc = 1
Box X = 81.282 Box Y = 66.041 Box Z = 74.628
Alpha = 90.000 Beta = 90.000 Gamma = 90.000
NFFT1 = 84 NFFT2 = 64 NFFT3 = 80
Cutoff= 10.000 Tol =0.100E-04
Ewald Coefficient = 0.27511
Interpolation order = 4
----------------------------------------------------------------------
+++++++++++++START_PART_OF_MY_OUTPUT+++++++++++++++++
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Received on Mon Aug 22 2016 - 04:00:02 PDT
