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 - 13:35:28 PDT
