> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Fri Jun 08 2018 - 05:30:02 PDT
