Hiv-A047 PMF

# 85.23 /home/databank_70t/lywu/hiv-1/a047/vsremd/test-100ns/pmf
scp lywu@172.21.85.24:/home/databank/lywu/trypsin/inhibitiors/trypsin-18/20replica/zzy-atom_center/pmf-2024-09-06-atomcenter.ipynb ./


(base) [dddc@localhost pmf]$ cat ../../../smd/smd.18.dat 
ligand: COM ATOMS=421,1990
active-residue: COM ATOMS=3139-3220
dist: DISTANCE ATOMS=active-residue,ligand
restraint-distance: RESTRAINT ARG=dist KAPPA=5000 AT=2
# monitor the two variables and the metadynamics bias potential
PRINT STRIDE=100 ARG=dist,restraint-distance.bias FILE=COLVAR




gmx_mpi trjconv -f ../md0/md.xtc -s ../md0/md.tpr -n ../../index.ndx -o dry.xtc -pbc mol -ur compact


# 25,124 2个ASP5