Hello, Emmanuel
Regarded with the implementation of ABMD to pmemd.cuda, the input format
has been changed to namelist style. You should define all the variables
inside the namelist &abmd, and also define Collective Variables in a CV
input file. All the details can be found in
http://ambermd.org/doc12/nfe.pdf
Please read the manual and change your input to the new style, also don't
forget to define infe=1 in the &cntrl namelist.
Best
Feng
On Mon, Aug 22, 2016 at 6:32 AM, Emmanuel <emmanuel.salawu.gmail.com> 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+++++++++++++++++
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Feng Pan
Ph.D. Candidate
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Mon Aug 22 2016 - 09:00:02 PDT
