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run_molecular_dynamics_simulation_from_minimized_structure [2016/03/07 14:22] (current)
root created
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 +====== 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!
  
run_molecular_dynamics_simulation_from_minimized_structure.txt · Last modified: 2016/03/07 14:22 by root