Hi Bill,
Yes. I think I am pointing the correct input file.
Regards,
Simon
2018-06-08 20:18 GMT+08:00 Bill Ross <ross.cgl.ucsf.edu>:
> > Indeed, there was no energy in restraint part. I should have checked that
> > earlier. But where exactly I missed in the input file?
>
> Does your cmdline arg point to the right mdin?
>
> Bill
>
> On 6/8/18 4:50 AM, Simon Kit Sang Chu wrote:
> > Dear all,
> >
> > Thanks for all your prompt reply. This is a section of the output file.
> >
> > ------------------------------------------------------------
> --------------------
> > 2. CONTROL DATA FOR THE RUN
> > ------------------------------------------------------------
> --------------------
> >
> > ACE
> >
> >
> > 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 = 100, ntrx = 1, ntwr =
> > 500000
> > 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 = 8.00000, intdiel = 1.00000
> >
> > Frozen or restrained atoms:
> > ibelly = 0, ntr = 0
> >
> > Molecular dynamics:
> > nstlim = 500000, nscm = 1000, nrespa = 1
> > t = 0.00000, dt = 0.00200, vlimit = 20.00000
> >
> > Langevin dynamics temperature regulation:
> > ig = 695414
> > temp0 = 300.00000, tempi = 0.00000, gamma_ln= 2.00000
> >
> > Pressure regulation:
> > ntp = 1
> > pres0 = 1.00000, 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 = 100
> >
> > Ewald parameters:
> > verbose = 0, ew_type = 0, nbflag = 1, use_pme =
> > 1
> > vdwmeth = 1, eedmeth = 1, netfrc = 1
> > Box X = 30.530 Box Y = 30.530 Box Z = 30.530
> > Alpha = 109.471 Beta = 109.471 Gamma = 109.471
> > NFFT1 = 32 NFFT2 = 32 NFFT3 = 32
> > Cutoff= 8.000 Tol =0.100E-04
> > Ewald Coefficient = 0.34864
> > Interpolation order = 4
> > .
> > .
> > .
> > ------------------------------------------------------------
> --------------------
> > 4. RESULTS
> > ------------------------------------------------------------
> --------------------
> >
> > ---------------------------------------------------
> > APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
> > using 5000.0 points per unit in tabled values
> > TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
> > | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
> > | CHECK d/dx switch(x): max rel err = 0.8332E-11 at 2.782960
> > ---------------------------------------------------
> > |---------------------------------------------------
> > | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
> > | with 50.0 points per unit in tabled values
> > | Relative Error Limit not exceeded for r .gt. 2.47
> > | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
> > | with 50.0 points per unit in tabled values
> > | Relative Error Limit not exceeded for r .gt. 2.89
> > |---------------------------------------------------
> >
> > NSTEP = 100 TIME(PS) = 20.200 TEMP(K) = 292.28 PRESS =
> > -1022.8
> > Etot = -4181.4073 EKtot = 1010.0270 EPtot =
> > -5191.4343
> > BOND = 3.0503 ANGLE = 24.7990 DIHED =
> > 30.8835
> > 1-4 NB = 8.0855 1-4 EEL = 101.2710 VDWAALS =
> > 737.2717
> > EELEC = -6096.7954 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > EKCMT = 490.7048 VIRIAL = 968.7697 VOLUME =
> > 21647.4104
> > Density =
> > 0.7980
> > Ewald error estimate: 0.1519E-03
> > ------------------------------------------------------------
> ------------------
> >
> >
> > NSTEP = 200 TIME(PS) = 20.400 TEMP(K) = 307.70 PRESS =
> > -622.6
> > Etot = -4156.1706 EKtot = 1063.3369 EPtot =
> > -5219.5076
> > BOND = 9.5860 ANGLE = 19.8155 DIHED =
> > 29.8152
> > 1-4 NB = 7.1849 1-4 EEL = 98.2946 VDWAALS =
> > 760.9049
> > EELEC = -6145.1087 EHBOND = 0.0000 RESTRAINT =
> > 0.0000
> > EKCMT = 518.2475 VIRIAL = 806.5117 VOLUME =
> > 21442.3978
> > Density =
> > 0.8057
> > Ewald error estimate: 0.8508E-04
> > ------------------------------------------------------------
> ------------------
> >
> >
> > Indeed, there was no energy in restraint part. I should have checked that
> > earlier. But where exactly I missed in the input file?
> >
> > I am not sure if there was a tutorial on how to apply restraints. I am
> > current learning by taking a complicated example on page 532 and the
> > command explanations in AMBER 2018 manual. I hope there would be more
> > intuitive way to learn distance and plane-point restraints.
> >
> > Regards,
> > Simon
> >
> > 2018-06-08 19:40 GMT+08:00 Stephan Schott <schottve.hhu.de>:
> >
> >> Hi,
> >> Is that exactly the input file you used? Because I see a exclamation
> mark
> >> in front of nmropt, which in practice is as having nmropt = 0. When
> >> restraints are correctly used there is a report of the parsing in the
> >> output header, and restraint energies are reported additionally to the
> >> usual energies.
> >> Hope it helps,
> >>
> >> 2018-06-08 13:32 GMT+02:00 Bill Ross <ross.cgl.ucsf.edu>:
> >>
> >>> What does the output file show of the restraint input? Copy/paste,
> >> please.
> >>> Bill
> >>>
> >>>
> >>> On 6/8/18 4:13 AM, Simon Kit Sang Chu wrote:
> >>>> Dear AMBER users,
> >>>>
> >>>> I am new to AMBER usage and I am trying to learn restraints in AMBER
> >>>> simulation. I made a simple run on two peptides (ACE-ALA-NME and
> >>>> ACE-PRO-NME) solvated. I am trying to set up distance restraint
> between
> >>> the
> >>>> two atoms in the corresponding peptide.
> >>>>
> >>>> Despite the setting, the trajectory showed that the restraint was not
> >>>> working. Would anyone mind to point out the missing part in the input
> >>> file?
> >>>>
> >>>> &cntrl
> >>>> imin = 0, ! no minimisation
> >>>> ntx = 5, ! restart with coordinate and velocity
> >>>> irest = 1, ! restart, which means velocity is expected
> in
> >>>> inpcrd
> >>>> nstlim = 500000,! number of steps (1 ns)
> >>>> dt = 0.002, ! step size
> >>>> ntf = 2, ! not to calculate force for SHAKE
> constrained
> >>> bonds
> >>>> ntc = 2, ! SHAKE for all hydrogen-bonded
> >>>> temp0 = 300.0 ! temperature
> >>>> ntpr = 100, ! info frequency
> >>>> ntwx = 10000, ! trajectory frequency
> >>>> cut = 8.0, ! cutoff
> >>>> ntb = 2, ! PBC for constant pressure
> >>>> ntp = 1, ! Berendsen barostat
> >>>> ntt = 3, ! Langevin thermostat
> >>>> gamma_ln=2.0, ! Langevin thermostat frequency
> >>>> ig = -1, ! random seed
> >>>> !nmropt = 1, ! read extra restraint input from external
> >>> DISANG
> >>>> file
> >>>> /
> >>>>
> >>>> &rst ! Distance restraint between index 18 23, gradually
> increasing
> >>> in
> >>>> time
> >>>> iat = 18, 23, ! iat nonzero up to two
> >> scalar >
> >>>> distance restraint
> >>>> nstep1 = 1, nstep2 = 500000, ! linear scaling of
> restraint
> >> in
> >>>> time
> >>>> iresid = 0, ! selecting atoms instead of
> >>> groups
> >>>> (default)
> >>>> ifvari = 1, ! time-dependent restraint
> >>>> coefficient
> >>>> ! potential form : 0--linear--r1--harmonic--r2--
> >>>> flat--r3--harmonic--r4
> >>>> r1 = 0., r2 = 1., r3 = 1., r4 = 99., rk2 = 0., rk3 = 0.,
> >>>> r1a= 0., r2a= 1., r3a= 1., r4a= 99., rk2a= 5., rk3a= 5.,
> >>>> /
> >>>>
> >>>> Thanks for your help.
> >>>>
> >>>>
> >>>> Regards,
> >>>> Simon
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> >> --
> >> Stephan Schott Verdugo
> >> Biochemist
> >>
> >> Heinrich-Heine-Universitaet Duesseldorf
> >> Institut fuer Pharm. und Med. Chemie
> >> Universitaetsstr. 1
> >> 40225 Duesseldorf
> >> Germany
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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Received on Fri Jun 08 2018 - 05:30:03 PDT
