[AMBER] restraint definitions

From: Jordi Bujons via AMBER <amber.ambermd.org>
Date: Fri, 22 Jul 2022 18:38:15 +0200


I am trying to simulate a system that includes a chloride bound ionophore
and a POPC membrane to study the anion transport process, but I find that
the anion is easily released into the water slab even if use restraints to
keep it bound. I wonder if the restraints are correctly defined. I am using
the following inputs for the production phase:

> cat Prod.in
Lipid production 303K 20ns
  imin=0, !Minimization is turned off
  ntx=5, !Read coordinates, velocities and box information
  irest=1, !Restart simulation from previous restat file
  ntc=2, !SHAKE on
  ntf=2, !SHAKE constrain bonds to hydrogen
  tol=0.0000001, !Relative geometrical tolerance for coordinate
resetting in shake
  nstlim=10000000, !number of MD steps
  ntt=3, !Langevin dynamics for temp control
  gamma_ln=1.0, !thermostat collision frequency of 1.0 ps-1
  temp0=303.0, !Final temp
  ntpr=5000, !write to output file every ntpr steps
  ntwr=500000, !write a restart file every ntwr steps
  ntwx=5000, !write to trajectroy file every ntwx steps
  dt=0.002, !time step in ps
  ig=-1, !random number seed
  ntb=2, !Use constant pressure PBC
  ntp=2, !anisotropic (x-,y-,z-) pressure scaling
  cut=10.0, !cutoff of 10 angstroms
  ioutfm=1, !write trajectory files in NetCDF format
  ntxo=2, !NetCDF output of the final coordinates, velocities,
and box size

> cat RST.dist
 &rst iat=1,17288,0
   r1=3.300000, r2=3.500000, r3=3.500000, r4=3.700000, rk2=5.000000,
   nstep1=0, nstep2=0,
 &rst iat=3,17288,0
   r1=3.300000, r2=3.500000, r3=3.500000, r4=3.700000, rk2=5.000000,
   nstep1=0, nstep2=0,
 &rst iat=54,17288,0
   r1=3.300000, r2=3.500000, r3=3.500000, r4=3.700000, rk2=5.000000,
   nstep1=0, nstep2=0,
 &rst iat=37,17288,0
   r1=1.850000, r2=1.970000, r3=1.970000, r4=2.100000, rk2=5.000000,
   nstep1=0, nstep2=0,

where atom 17288 is the chloride and atoms 1, 3, 37 and 54 are from the
ionophore molecule. Is there anything wrong with these inputs?

Thanks for any comments.


Jordi Bujons, PhD
Dept. of Biological Chemistry (QB)
Institute of Advanced Chemistry of Catalonia (IQAC)
National Research Council of Spain (CSIC)
Address: Jordi Girona 18-26, 08034 Barcelona, Spain
Phone: +34 934006100 ext. 437684
               (direct) +34 934006143
FAX: +34 932045904

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Received on Thu Aug 04 2022 - 13:35:28 PDT
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