AMBER Archive (2002)

Subject: about solvateOct

From: Nikolai Smolin (smolin_at_steak.chemie.uni-dortmund.de)
Date: Fri Jul 19 2002 - 03:22:20 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 iso 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