AMBER Archive (2001)

Subject: RE: periodic box size

From: Guanglei Cui (cuigl_at_morita.chem.sunysb.edu)
Date: Fri Feb 16 2001 - 12:30:27 CST

Hi,
    In amber6, the box information from restart files will override A, B,
and C in your input file. The box information specified in your input file
will override that of parm file. If you're using older version, I remember
the box size should be better dividable by 2, 3 or 5 to make the calculation
faster. The larger the box size, more time is needed. Perhaps it's automatic
in amber6 now.

Regards,

Guanglei Cui

-----Original Message-----
From: Raja Swaminathan [mailto:rajaamber6_at_rediffmail.com]
Sent: Friday, February 16, 2001 12:25 PM
To: amber_at_cgl.ucsf.edu
Subject: periodic box size

hi amber users
i have done md simulations on a 14 mer DNA duplex.
the box size is

42.7539974 43.0651857 45.8525446

i have used the next line as 43 43 46

will it be there any problem in md simulations or
the system will take only more computational time.

thanks

raja

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