amber tutorials
crown tutorial

Crown ether with ion - equilibration and dynamics

Equilibration

In vacuum, a topologically constrained molecule such as the crown ether does not need careful equilibration, so here it is warmed up directly to 300K. 

  Equilibrate the system:

    % sander_classic -O \
            -i md0.in \
            -p ../setup/crowni.top \
            -c ../setup/crowni.crd \
            -o md_na.out \
            -x md_na.crd \
            -r md_na.rst

  Extract some ensemble characteristics:

    % egrep Etot  md_na.out | awk '{print (NR-1) * 0.2, $3}' > en_md_na.gr
    % egrep NSTEP md_na.out | awk 'NF==12 {print $6, $9}'    > te_md_na.gr
Looking at the ensemble characteristics, which were graphed using xmgr:

Demo by Bill Ross.