Subject: Two questions about MD and NAMD2.2!

From: Hung-Chung Huang <[email-masked]>
Date: Tue, 06 Feb 2001 12:29:39 -0600

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

---

From: Jim Phillips <[email-masked]>
Date: Tue, 6 Feb 2001 15:26:23 -0600 (CST)

> Berendsen pressure bath coupling, and no PME.

Did you set non-zero temperature coupling coefficients somewhere?  If you
don't do this, it will default to a column in your coordinates pdb file,
which will probably be zero.  This will result in none of the atom being
coupled to the temperature bath.

> close to the protein for PME?

The option wrapWater only effects output coordinates and is only there
because visualizers are ignorant of the periodic cell.  Your ions are
diffusing between images, which is normal.  What makes you say that your
ions are causing problems?

-Jim