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
Received on Fri Jun 08 2018 - 05:00:02 PDT
