Guide for Steered Molecular dynamics (SMD) simulation on ASU Sol cluster

Initial steps with PDB

Follow the PyMOL guide here: PyMOLGuide

Using VPN to connect to ASU network:

Follow the VPN guide here: VPNGuide

After logging in:

pwd shows me home directory /home/ikazan

change directory to scratch space

cd /scratch/ikazan

create a new directory here by using

mkdir -pv testdir1

change directory to the new one

cd testdir1/

ls

the directory is empty

pwd shows me the current working directory

copy the SMD directory on github to the /scratch/ikazan/testdir1 directory on sol. Run the command on the terminal connected to your local computer.

scp -r SMD ikazan@login.sol.rc.asu.edu:/scratch/ikazan/testdir1/

prepare SMD

Swtich terminal window to the one connected to sol and run

cd SMD

cd prepare

From the production MD simulation copy the parameter file WT_cript_S102Y.parm and the last pdb file last_prod.pdb in to this directory.

run

sbatch pull_prepare.sh [62] [123 125 127] 3 0.0001 25

(sbatch pull_prepare.sh <FIX> <SMD> <k> <Vel> <dis> )

we will copy the prepared files to required_files directory

cp -v WT_cript_S102Y.parm ../required_files/
cp -v last_prod.pdb ../required_files/
cp -v WT_cript_S102Y_rest.pdb ../required_files/
cp -v WT_cript_S102Y_SMD.ref ../required_files/

then

cd ..

run SMD

run 50 pulls

circle_run.sh 1 50