SA Simulation

SA Simulation

What can we do with simulated annealing simulation?

To run simulated annealing on Bridges using Gromacs:

1. Open a terminal and log in to bridges2:

ssh -l jcai07 bridges2.psc.xsede.org -p 2222

or ssh -l yohei bridges2.psc.edu

2. Transfer file to Bridges, in the charmm-gui tar file floder open a terminal:

sftp jcai7@data.bridges.psc.edu

or sftp yohei@bridges2.psc.edu

Use cd to move around in your Bridges2 account

Use lcd to move around on your local computer

put 3emlCharmm-gui.tgz

3. Move charmm-gui tar file to $SCRATCH and unpack it.

mv 3emlCharmm-gui.tgz $SCRATCH

cd $SCRATCH

tar zxvf 3emlCharmm-gui.tgz

4. Rename unpacked file.

mv 3emlCharmm-gui-15someNumber 3emlSaAug15

5. Prepare files.

cd 3emlSaAug15/gromacs

cp /home/jcai7/saFile/step6.1_equilibration.mdp /home/jcai7/saFile/step6.2_equilibration.mdp /home/jcai7/saFile/step7_production.mdp /home/jcai7/saFile/README /home/jcai7/saFile/equi.slu /home/jcai7/saFile/gromacs.slu $PWD

6. Run equilibration.

sbatch equi.slu

7. Run production run. (Example of directory: cd $HOME/simulation/membrane/SA)

sbatch SA-production.slu

Storage

cd /ocean/projects/mcb200111p/yohei/

After the production run, there is md.part0001.xtc file, which is the trajectory file. Due to the atoms crossing the periodic boundaries, there are lines in the protein in the trajectory file. To fix it, run:

module load cuda/9.2 gcc/7.3.0

source /home/jcai7/Library/gromacs/versions/2018.3/cuda-9.2/gcc-7.3.0/threads/bare/bin/GMXRC

gmx trjconv -f md.part0001.xtc -s step7_production.tpr -o pbc.xtc -pbc mol -ur compact -center

Choose 1 (protein) to group to the center for the first ask, choose 0 (the system) for output for the second ask.

gmx trjconv -f pbc.xtc -s step7_production.tpr -o processed.xtc -fit rot+trans

Choose the same options as the last step.

The first command would center the protein in the box and the last would remove translation and rotation making it easier to visualize.

To get protein structure in the last frame of the trajectory file (there are 1000 frame, so the last frame is frame1000, -b 1000 -e 1000):

module load cuda/9.2 gcc/7.3.0

source /home/jcai7/Library/gromacs/versions/2018.3/cuda-9.2/gcc-7.3.0/threads/bare/bin/GMXRC

gmx trjconv -f processed.xtc -s step7_production.tpr -o sa_protein.pdb -center -ur compact -pbc mol -b 1000 -e 1000

Choose 1 and then 1.

Copy output files of molecular dynamic simulation to home directory, so that you can transfer output files to local computer.

cp processed.xtc sa_protein.pdb step6.6_equilibration.gro step7_production.tpr /home/jcai7/saAnalysis