Hi,
I wish to run a simulation (min, heat, equil) in vacuum, but my script doesn’t seem to work. Can anyone help me with it? Thanks. The protein which I’m simulating is 31 residues. I’m doing this simulation so as to obtain an initial coiled-coil structure for REMD.
#### Minimize Protein
cat << EOF > mdin
#The whole system minimization
&cntrl
imin=1,
maxcyc=5000,
ncyc=1000,
ntb=0,
ntr=0,
cut=999.,
rgbmax=999.,
igb=6,
drms=0.01,
ntpr=50,
/
EOF
/usr/local/openmpi/bin/mpirun -np $NCPUS -machinefile $PBS_NODEFILE sander.MPI -O -i mdin -o min.out -p 1q2k_dry.top -c 1q2k_dry.crd -r min.rst -ref 1q2k_dry.crd </dev/null
#### Heating I
cat << EOF > mdin
#Heating up the system, 2.0fs time step
&cntrl
nstlim=5000, dt=0.002, ntx=1, irest=0, ntpr=50, ntwr=50, ntwx=50,
tempi =0.0, temp0=400.0, ntt=3, gamma_ln=4.0, tautp=2.0, ig=71277,
ntb=0, ntp=0,
ntc=2, ntf=2,
ntr=0, igb=6,
cut=999., rgbmax=999.,
/
EOF
/usr/local/openmpi/bin/mpirun -np $NCPUS -machinefile $PBS_NODEFILE sander.MPI -O -i mdin -o heat.out -p 1q2k_dry.top -c min.rst -r heat.rst -x heat.mdcrd -ref min.rst -inf mdinfo </dev/null
#### Equilibration 1
cat << EOF > mdin
#Constant pressure constant temperature
&cntrl
nstlim=500000, dt=0.002, igb=6, ntx=7, irest=1, ntpr=500, ntwr=5000, ntwx=500,
temp0=400.0, ntt=3, gamma_ln=4.0, tautp=2.0,
ntb=0, pres0=1.0, ntp=1, taup=2.0,
ntc=2, ntf=2,
ntr=0, nbflag=0, nsnb=999,
cut=999., rgbmax=999.,
/
EOF
/usr/local/openmpi/bin/mpirun -np $NCPUS -machinefile $PBS_NODEFILE sander.MPI -O -i mdin -o equ.out -p 1q2k_dry.top -c heat.rst -r equ.rst -x equ.mdcrd -ref heat.rst -inf mdinfo </dev/null
Regards
Yip Yew Mun
Graduate, PhD
Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University
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Received on Sat Nov 16 2013 - 07:30:02 PST
