Dear all,
I am trying to simulate polymer water interactions. I have a water (TIP3P) layer of thickness of 50 Angstrom, over that a polymer layer of 40 Angstrom, then a vacuum layer of 160 Angstrom. The vacuum layer is to maintain 2D boundary condition.
After minimization, the system was subjected to NVT equilibration at 300K.
The water molecules tend to leave the water layer, penetrate through polymer and escape into the vacuum.
Whether this condition is normal or it is kind of system instability? If it is system instability, then is there any method to arrest the water molecules from entering into the vacuum.
Thank you,
Dear Santosh,
In my experience, water tends to stick to itself even facing vacuum, so something in you system is going wrong.
Regards
Tatiana Kuznetsova
University of Bergen
Dear all,
I am trying to simulate polymer water interactions. I have a water (TIP3P)
layer of thickness of 50 Angstrom, over that a polymer layer of 40 Angstrom,
then a vacuum layer of 160 Angstrom. The vacuum layer is to maintain 2D
boundary condition.
After minimization, the system was subjected to NVT equilibration at 300K.
The water molecules tend to leave the water layer, penetrate through polymer
and escape into the vacuum.
Whether this condition is normal or it is kind of system instability? If it
impossible to say with so few details. there are many things that can
be checked to see if a simulation is working correctly.
have you checked that your parameters are correct?
can you reproduce published data with each component of your system,
water/polymer, independently?
has each of the subsystems been properly equilibrated before you merged them?
is your choice of time step adequate? can your simulation conserve
energy with fix nve?
is system instability, then is there any method to arrest the water
molecules from entering into the vacuum.
you can use things like fix wall/reflect or fix oneway to turn the
waters around. that may be acceptable as a temporary "equilibration
aide", but if you simply force your system to look the way your want
and not let it ultimately go where the physics of the model wants it
to, then you are no longer doing research but making an animation.
axel.