Research:amber tips pr

Ren's example for running sander and pmemd

Executables

Oscar's mod sander in /home/oscar/data2-oscar mod pmemd in /home/oscar/pmemd/src

example mdin and run script files in /home/pren/AMOEBA/solvation/compare/

A Quick Guide

       TO run sander:
       xyzpdb ele.xyz
       analyze box30 PC > ele.analout
       /opt/amber/bin/amoeba_parm -name ele -title "water" > ele.amoeba_parm.out
       /opt/amber/bin/sander -i ele.mdin -c ele.inpcrd -p ele.prmtop -o mdout &

       To run pmemd:
       /opt/mpich2-fc7/bin/mpdboot -n 1 -f ./host --ncpus=4
       /opt/mpich2-fc7/bin/mpirun -n 4 /home/pren/pmemd-oscar/src/pmemd -i ele.mdin -c ele.inpcrd -p ele.prmtop -o mdout.nvt.pmemd -r restrt.pmemd 2>/dev/null &

       remmeber octahedron require mods in inpcrd (angle) and prmtop ("2" and angle)

direcories in /home/pren/AMOEBA/solvation/compare/

cube:                             nvt, cubic water box bysander8

cube-pme:                      nvt, pmemd 9

sander-nvt:                      truncated octahedron (TO) long nvt run, sander 8

pmemd-nvt:                    TO, nvt, pmemd 9

sander-long-npt:              truncated octahedron long npt run sander 8

pmemd-test-npt:              short npt, TO, pmemd

pmemd-nvt/

       check softcore parameters defaults in pmemd (sander has initilized correctly).
       i.e. without softcore-line lines in mdin, lig_idx is initialized to 0 so it is fine.
       softcore-print usem pmemd from ~/pmemd-sun