Table of Contents

Run MD from minimized structure

First, download the 7 input files needed:

Now, let your already prepared files be and rec.crd. And also, your final restart file from minimization be rec.h.rst. Execute the following sequence of commands:

pmemd -O -i -o h.out -p -c rec.h.rst -x rec.h.mdcrd -r rec.eq0.rst -ref rec.h.rst
pmemd -O -i -o eq1.out -p -c rec.eq0.rst -x rec.eq1.mdcrd -r rec.eq1.rst -ref rec.eq0.rst
pmemd -O -i -o eq2.out -p -c rec.eq1.rst -x rec.eq2.mdcrd -r rec.eq2.rst -ref rec.eq1.rst
pmemd -O -i -o eq3.out -p -c rec.eq2.rst -x rec.eq3.mdcrd -r rec.eq3.rst -ref rec.eq2.rst
pmemd -O -i -o eq4.out -p -c rec.eq3.rst -x rec.eq4.mdcrd -r rec.eq4.rst -ref rec.eq3.rst
pmemd -O -i -o eq5.out -p -c rec.eq4.rst -x rec.eq5.mdcrd -r rec.eq5.rst -ref rec.eq4.rst
pmemd -O -i -o md1.out -p -c rec.eq5.rst -x rec.md1.mdcrd -r rec.md1.rst

Then, to continue another 200ps of simulation:

pmemd -O -i -o md2.out -p -c rec.md1.rst -x rec.md2.mdcrd -r rec.md2.rst

Now if you need a pdb to see the final state of the simulation:

ambpdb -p < rec.md1.rst > md1.pdb

That's all folks!