Two questions about MD and NAMD2.2!

[Hung-Chung Huang <HCHuang "at@at" UH.EDU>]

 Dear CCLers,
I have two questions about running MD simulations with NAMD 2.2 from
 UI
 (http://www.ks.uiuc.edu).
1. After I finished 60ps equilibration  by using  temperature
 reassignment method (from 50K to 300K gradually)  of NAMD2.2, the
 system
 looked very stable around 300K (especially in the last 20ps of
 equilibration). But why the system's temperature kept increasing after
 I
 went to the MD phase simulations? P.S., I used temperature coupling ,
 Berendsen pressure bath coupling, and no PME.
2. When I tried PME and if I positioned the ions (e.g. sodium ions) on
 the edge of water box, the ions would leave the box and cause problems.
 Is there any way to confine the sodium ions in the box (e,g., with
 "wrapWater" on, waters can be wrapped back to another side of
 box if
 they move out of the box)? Or what's the criterion to position ions
 close to the protein for PME?
 Your hints or suggestions will be much appreciated!!!
 Joe
 --
 http://adrik.bchs.uh.edu/~jhuang