time the minimization includes solute under weak restraints (force
constant equal to 10 kcal/mol/A ̊^2 ):
Initial energy minimization—step 2 (solvent and restrained
solute)
&cntrl
imin=1, ncyc=500, maxcyc=2000,
ntb=1, cut=12, ntr=1
/
Weak restraints
10.0
RES 1 291
END
END
In the third stage we perform a short MD run of theNVT
ensemble (ntb¼1), i.e., keeping the number of molecules (N),
volume (V), and temperature (T) constant. The integration step is
equal to 1 fs, and during the run we increase the temperature from
0 K to 300 K:
MD 20 ps with weak restraints and step of 1 fs
&cntrl
imin=0, irest=0, ntx=1,
ntb=1, cut=12, ntr=1,
ntc=2, ntf=2,
tempi=0.0, temp0=300.0,
ntt=3, gamma_ln=1.0,
nstlim=20000, dt=0.001,
ioutfm=1, ntxo=2,
ntpr=1000, ntwx=1000, ntwr=1000
/
Weak restraints
10.0
RES 1 291
END
END
The ioutfm¼1 keyword indicates the binary output trajectory
in the NetCDF format. Similarly, ntxo¼2 creates the restart file in
the NetCDF format. The keywords ntpr, ntwx and ntwr define the
frequency of writing to the output file, to the trajectory file and to
the restart file, respectively. In this case we see new output every
1000 steps of 1 fs each, i.e., with the interval of 1 ps. In the next
stage of the protocol we perform a somewhat longer MD run on
the NPTensemble (ntb¼2), i.e., keeping the number of molecules
(N), pressure (P), and temperature (T) constant. We use the
Molecular Dynamics in Virtual Screening 153