I take that back, ncsu_abmd doesn't use namelist apparently.
Looks like that code was falling out of use back in 2012:
http://archive.ambermd.org/201208/0361.html
Bill
On 8/22/16 3:45 AM, Bill Ross wrote:
> I think your namelist format may be wrong - there should be '&'s in there?
>
> Bill
>
>
> On 8/22/16 3:32 AM, Emmanuel wrote:
>> 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+++++++++++++++++
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Aug 22 2016 - 04:00:03 PDT
