[gmx-users] shell dynamics

[qiao rui]

Thanks David for the quick reply.

The temperature increase is observed during the first few pico second, and
after that it is normal (I did not run it too long yesterday).

I installed version 3.2, but this time grompp pops a new error:
"Water polarization should now be listed under [ water_polarization ]".
I am assuming that the .itp file for the SW model has some problem. How do
I modify the .itp file?

I have two addition questions:
1. if I have other molecules in the system, should the shell atom interact
with them?

2. To my impression, one first need to equilibrate system using shell
minimization for a while (say, 50ps, using time step 1fs), and then one
can switch to LP model (using time step 0.2 fs). To switch to LP model,
can I simply increase the emtol to 100 so that no optimization is done?

by the way, the simulation is kind of slow for even a small system (900
water molecules -> 200 hours/1ns), is this normal?

Thanks for your help!

sincerely,

Rui
------------------------
Rui Qiao
Research Assistant
Beckman Institute, UIUC