AMBER Archive (2002)

Subject: correction about solvateOct

From: Nikolai Smolin (smolin_at_steak.chemie.uni-dortmund.de)
Date: Fri Jul 19 2002 - 04:09:58 CDT

Dear AMBER users:

I have question about solvateOct command
in Leap and I used AMBER 6,0.
I did not understand what means 'iso' option in this command.
If I want to use in my simulation PME is it necessary to use
this option for preparation my box or not?
I tried with this option and without . And I recieved different number
atoms in my system:

alignAxes protein
solvateOct protein WATBOX216 12,0 iso 0,75 in this case 28223 atoms
in box

alignAxes protein
solvateOct protein WATBOX216 12,0 0,75 in this case 19748 atoms in box

What I made wrong?
Or it is correct?
What way for preparation box with less number of particles perfect?

Tnaks in advance!! 

-- 
Dipl.-Phys. Nikolai Smolin

Physikalische Chemie I
Universitaet Dortmund
Otto-Hahn-Str. 6
44221 Dortmund
Germany

Tel:     +49 / 231 / 755 3929
Fax:     +49 / 231 / 755 3901

E-mail:  smolin_at_steak.chemie.uni-dortmund.de