Dear professor,
A MD simulation was run on procs 8, under NPT ensemble. Each methane molecule was seen as an United atom, and TIP4P/Ice forcefield was adopted for water molecules.
In the whole simulation, no error occurred, and the total energy evolution with time was monitored. In the beginning, the total energy dropped sharply from 15867 to -11236 within 0.004ns,then subsequently, it kept almost constant. Here is a problem that the outputs suggested O-H bond in some water molecules broke shortly after the simulation started. The accessories are input script, data file. So could you please give me a cue? Thank you a lot!
Yours,
Tang
in.ch4 (2.34 KB)
data.data (356 KB)
2011/5/9 tlx0509236.happy <[email protected]...>:
Dear professor,
A MD simulation was run on procs 8, under NPT ensemble. Each methane
molecule was seen as an United atom, and TIP4P/Ice forcefield was adopted
for water molecules.
In the whole simulation, no error occurred, and the total energy evolution
with time was monitored. In the beginning, the total energy dropped sharply
from 15867 to -11236 within 0.004ns,then subsequently, it kept almost
you obviously started from a very high potential energy configuration that
then quickly relaxed. it would have probably been better to run some steps
of minimization first to "take off the edge".
constant. Here is a problem that the outputs suggested O-H bond in some
water molecules broke shortly after the simulation started. The accessories
why not? you are started obviously from a non-equilibrium configuration
and you run at a temperature above the boiling point. what do you expect?
are input script, data file. So could you please give me a cue? Thank you a
lot!
do you expect somebody do redo your simulation, only because you
found something that you cannot explain??? please think again!
but there is one thing that i can say without even running your intput.
you use fix npt _and_ fix temp/rescale. why? that will guarantee that
your trajectory will be unphysical and thus worthless.
axel.