That would be a minimal reason. Beyond that, the solution as mentioned
by Stephan Schott,
> I see a exclamation mark in front of nmropt, which in practice is as having nmropt = 0.
!nmropt = 1, ! read extra restraint input from external
Bill
On 6/8/18 5:22 AM, Simon Kit Sang Chu wrote:
> 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
>>>>>> _______________________________________________
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>>>>>> 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
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>>>>
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>>
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Received on Fri Jun 08 2018 - 06:00:03 PDT
