[AMBER] Enquiries about running a simulation in vacuum

From: Yip Yew Mun <yipy0005.gmail.com>
Date: Sat, 16 Nov 2013 22:57:49 +0800

Hi,

I wish to run a simulation (min, heat, equil) in vacuum, but my script doesnít seem to work. Can anyone help me with it? Thanks. The protein which Iím simulating is 31 residues. Iím 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
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