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(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of Timex. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)

5.5 Case Study - Folding TRP Cage (Advanced analysis and clustering) - SECTION 5

By Ross Walker

Stage 5: Production MD

The final stage of the simulation part of this tutorial is to run a long production simulation at 325 K. In the paper they run 50 ns of simulation at 325 K, but present results for only the first 20 ns, simply stating that the remaining 30 ns showed no significant change from the first part of the simulation. We shall run a similar 50 ns simulation even though the authors saw that the system folded within 5 ns to 20 ns:

"Two independent simulations converged to essentially identical families of structures after 5 and 20 ns."

We will run this 50 ns simulation in 10 stages of 5 ns each.  The reason we run it in 10 separate stages is this makes it much easier to resume the simulation should we experience a system crash. It also keeps the output and nc files to manageable sizes. We shall use an identical input file for all 10 stages. The input file is as follows:

 equil.in ```Stage 2 equilibration 1 0-5ns &cntrl imin=0, irest=1, ntx=5, nstlim=2500000, dt=0.002, ntc=2, ntf=2, ntt=1, tautp=0.5, tempi=325.0, temp0=325.0, ntpr=500, ntwx=500, ntb=0, igb=1, cut=999.,rgbmax=999. /```

Each of the 10 stages will consist of 2,500,000 steps (nstlim) with a 2 fs time step (dt) giving 5 ns per stage. Note we have SHAKE on the whole time (ntc=2, ntf=2), we use the Berendsen thermostat for temperature control (ntt=1) and now that we have heated our system up and it appears to be stable we can use a much more closely coupled thermostat of 0.5 ps (tautp=0.5). This will serve to keep our system close to 325 K. We set our target temperature at 325K as they do in the paper and we write to the output file and nc file every 500 steps. Writing more frequently that this would result in huge files. The nc file for each 5 ns is 35 Mb as it is. Every 500 steps should be frequent enough for our purposes.

Here is the PBS script I used to run the 10 jobs, you can modify it for your system:

```#PBS -l ncpus=16
#PBS -l walltime=500:00:00
#PBS -l cput=8000:00:00
#PBS -j oe
setenv AMBERHOME /usr/people/rcw/amber9
cd ~rcw/production
mpirun -np 16 \$AMBERHOME/bin/sander -O -i equil.in -p TC5b.prmtop -c heat7.ncrst -r equil1.ncrst -o equil1.out -x equil1.nc
gzip -9 equil1.nc
mpirun -np 16 \$AMBERHOME/bin/sander -O -i equil.in -p TC5b.prmtop -c equil1.ncrst -r equil2.ncrst -o equil2.out -x equil2.nc
gzip -9 equil2.nc
mpirun -np 16 \$AMBERHOME/bin/sander -O -i equil.in -p TC5b.prmtop -c equil2.ncrst -r equil3.ncrst -o equil3.out -x equil3.nc
gzip -9 equil3.nc
mpirun -np 16 \$AMBERHOME/bin/sander -O -i equil.in -p TC5b.prmtop -c equil3.ncrst -r equil4.ncrst -o equil4.out -x equil4.nc
gzip -9 equil4.nc
mpirun -np 16 \$AMBERHOME/bin/sander -O -i equil.in -p TC5b.prmtop -c equil4.ncrst -r equil5.ncrst -o equil5.out -x equil5.nc
gzip -9 equil5.nc
mpirun -np 16 \$AMBERHOME/bin/sander -O -i equil.in -p TC5b.prmtop -c equil5.ncrst -r equil6.ncrst -o equil6.out -x equil6.nc
gzip -9 equil6.nc
mpirun -np 16 \$AMBERHOME/bin/sander -O -i equil.in -p TC5b.prmtop -c equil6.ncrst -r equil7.ncrst -o equil7.out -x equil7.nc
gzip -9 equil7.nc
mpirun -np 16 \$AMBERHOME/bin/sander -O -i equil.in -p TC5b.prmtop -c equil7.ncrst -r equil8.ncrst -o equil8.out -x equil8.nc
gzip -9 equil8.nc
mpirun -np 16 \$AMBERHOME/bin/sander -O -i equil.in -p TC5b.prmtop -c equil8.ncrst -r equil9.ncrst -o equil9.out -x equil9.nc
gzip -9 equil9.nc
mpirun -np 16 \$AMBERHOME/bin/sander -O -i equil.in -p TC5b.prmtop -c equil9.ncrst -r equil10.ncrst -o equil10.out -x equil10.nc
gzip -9 equil10.nc
echo "DONE"```

All 10 stages take a total of about 27 hours to run on 16 cpus of a 1.3GHz SGI Altix. Here are the output files, you can download them individually or as a single tar.gz file (Warning the nc files are over 13Mb each compressed):

 Heating Stage Output File Restrt File Nc File Stage 1 equil1.out equil1.ncrst equil1.nc Stage 2 equil2.out equil2.ncrst equil2.nc Stage 3 equil3.out equil3.ncrst equil3.nc Stage 4 equil4.out equil4.ncrst equil4.nc Stage 5 equil5.out equil5.ncrst equil5.nc Stage 6 equil6.out equil6.ncrst equil6.nc Stage 7 equil7.out equil7.ncrst equil7.nc Stage 8 equil8.out equil8.ncrst equil8.nc Stage 9 equil9.out equil9.ncrst equil9.nc Stage 10 equil10.out equil10.ncrst equil10.nc Complete file set production.tar.gz (132 Mb)

You should load the nc files into VMD (unzip them first, it may take a while to load them. Perhaps one day the VMD authors will add support for reading compressed files <hint hint>). You can then watch the complete trajectory.  It is best if you choose ribbons as the representation. Here is one such structure coloured by residue type: