Computational Drug Discovery and Design

huge output trajectory files. It is for this reason that we use the

NetCDF format, which roughly halves the original volume of the

ASCII files (seeNote 5).

3.3 Running the MD
Simulation

1. Create a script that will launch all MD stages automatically.
   Here is an example of such a script, named
   “Run_pmemd_cuda”:

#!/bin/sh

#

# Setup of AMBER CUDA jobs.

# Each job needs:

# - mdinX (X is the current job number)

# - $BASE.prmtop (topology file)

# - ${BASE}Y.rst (Y=X-1, coordinate file)

# NOTE: the 1st coordinate file may be the original inpcrd

file.

#

# Each job creates:

# - ${BASE}X.out (output file)

# - ${BASE}X.rst (last coordinates)

# - ${BASE}X.mdcrd (trajectory)

#

# The CUDA version launches the tasks on a GPU. To select a

given

# device, use deviceQuery, then set CUDA_VISIBLE_DEVICES.

#

echo -n "Total number of jobs: "

read Njobs

echo -n "ID of the 1st job [1]: "

read MDfirst

echo -n "Basename for I/O files: "

read BASE

echo "List of available GPUs:"

deviceQuery -noprompt | egrep ’^Device’ |

while read dev; do

echo " "$dev

done

echo -n "Enter device #: "

read GPU

export CUDA_VISIBLE_DEVICES=$GPU

#

echo "Launching jobs on GPU #"$GPU"..."

if [ 0$MDfirst -eq "0" ]

then

MDfirst=1

fi

Molecular Dynamics in Virtual Screening 155