[gmx-users] David, questions about a polarized model.

xieyh at hkusua.hku.hk xieyh at hkusua.hku.hk
Mon Apr 4 15:52:10 CEST 2005

Dear Dr. David:

Thanks for your previous helps.

Based on your shell model for water, I used this concept in my simulated
molecule (not water). Differently, I gave the shell particle a small mass (e.g.
0.1 a.u), and also built some dummies to connect with shell particles for the
purpose of defining the polarizability.

However, in my simulation, once I adopted PME algorithm, then some common errors
such as "segmentation fault" "Lincs warning" or "pressure scaling is more than
1%" will be occurred. Actually, I have tried a lot ways to adjust some of
parameters. However, these problem can not yet solved. Any suggestion?

By the way, if I used "cut-off" for coulombtype, the simulation can be finished.
But, the shell particles moved a large distance. Is it because of the small
mass of particles, or other reasons? Could you give me some helps?

Thanks a lot.

Xie YH
HongKong Univ.

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