CHARMM Development Project Forums User Discussion & Questions Setup, I/O, and Basic questions entropy calculation:

Hello,

Is there a script to compute molecular mechanics entropy using CHARMM from a trajectory?

Thanks,
Preeti

Use the QUASiharmonics command in the VIBRAN module (vibran.doc).
Note that you need a fairly long trajectory for this to converge, and you have to remove overall translation/rotation from the trajectory first, then something like this would get you the quasiharmonic entropy:

coor dyna firstu 51 nunit 1 begin 500 stop 1000000 skip 500 sele segid prot end
calc nmodes = 3 * ?NSEL
bomlev -2 ! we will go beyond the deault limit of 3600 modes
vibran nmode @nmodes
quasi firstu 51 nunit 1 begin 500 stop 1000000 skip 500 sele segid prot end -
thermo resi temp 300