What does the mdout say when it reads the restraint file? It should tell
you.
On Fri, Jul 22, 2022, 12:38 PM Jordi Bujons via AMBER <amber.ambermd.org>
wrote:
> Hi,
>
> 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
> &cntrl
> 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
> nmropt=1
> /
> /
> &wt
> type='END',
> &end
> DISANG=RST.dist
>
> > cat RST.dist
> &rst iat=1,17288,0
> r1=3.300000, r2=3.500000, r3=3.500000, r4=3.700000, rk2=5.000000,
> rk3=5.000000,
> nstep1=0, nstep2=0,
> &end
> &rst iat=3,17288,0
> r1=3.300000, r2=3.500000, r3=3.500000, r4=3.700000, rk2=5.000000,
> rk3=5.000000,
> nstep1=0, nstep2=0,
> &end
> &rst iat=54,17288,0
> r1=3.300000, r2=3.500000, r3=3.500000, r4=3.700000, rk2=5.000000,
> rk3=5.000000,
> nstep1=0, nstep2=0,
> &end
> &rst iat=37,17288,0
> r1=1.850000, r2=1.970000, r3=1.970000, r4=2.100000, rk2=5.000000,
> rk3=5.000000,
> nstep1=0, nstep2=0,
> &end
>
> 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
>
>
>
>
> ----------------------------------------------------------------------------
> ----------
> 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
> jordi.bujons.iqac.csic.es
> http://www.iqac.csic.es
>
>
>
>
>
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Received on Thu Aug 04 2022 - 13:35:29 PDT
