Re: CCL:Two questions about MD and NAMD2.2!

[Jim Phillips <jim %-% at %-% ks.uiuc.edu>]

On Tue, 6 Feb 2001, Hung-Chung Huang wrote:
 > 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.
 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.
 > 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?
 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