Run MD from minimized structure

First, download the 7 input files needed:

• h.in. Heating. From 100K to 300K. 20ps Cα constrained simulation (k=20.0)
• eq1.in. 20ps 300K Cα constrained simulation (k=20.0)
• eq2.in. 20ps 300K Cα constrained simulation (k=15.0)
• eq3.in. 20ps 300K Cα constrained simulation (k=10.0)
• eq4.in. 20ps 300K Cα constrained simulation (k=5.0)
• eq5.in. 20ps 300K unconstrained simulation
• md.in. 200ps 300K simulation for production

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

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

Then, to continue another 200ps of simulation:

pmemd -O -i md.in -o md2.out -p rec.top -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.top < rec.md1.rst > md1.pdb

That's all folks!