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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Received on Fri Jun 08 2018 - 05:00:01 PDT
