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From: Bill Ross <ross.cgl.ucsf.edu>

Date: Fri, 8 Jun 2018 05:18:32 -0700

*> 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 - 05:30:02 PDT

Date: Fri, 8 Jun 2018 05:18:32 -0700

Does your cmdline arg point to the right mdin?

Bill

On 6/8/18 4:50 AM, Simon Kit Sang Chu wrote:

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Received on Fri Jun 08 2018 - 05:30:02 PDT

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