Dear Dave,
I did Langevin dynamics simulations with an alanine dipeptide molecule to
examine the effect of stopping COM motion. A box of 60*60*60 was set to
avoid the molecule from flying away. With gamma_ln=10/ps, temp0=400K,
IPS=1, and nstlim=100,000,000, I get the following average temperature:
nscm(steps) 0 10 30 100
300 1000
Average temperature(K): 399.65 404.67 411.53 421.19
425.82 427.51
Fluctuation of temperature(K): 84.20 87.31 87.99 89.43
90.00 90.18
Average potential energy(kcal/mol): -5.6077 -5.6027 -5.6128 -5.6062
-5.6141 -5.6081
Fluctuation of potential energy: 3.5986 3.6007 3.5976 3.6004
3.5975 3.6007
I checked the outputs and did not see any thing wrong with the
simulations.
These results indicating that removing COM motion can result in
inconsistence in simulation temperature. However, Average potential
energies are fine. That is, kinetic properties may be affected while
ensemble averaging properties may not. Therefore, for the purpose of
kinetic studies, COM stopping would not be recommended.
Thanks!
Xiongwu
Received on Wed Apr 05 2006 - 23:49:57 PDT
