RE: periodic box size

From: Guanglei Cui <>
Date: Fri 16 Feb 2001 13:30:27 -0500

    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.


Guanglei Cui

-----Original Message-----
From: Raja Swaminathan []
Sent: Friday, February 16, 2001 12:25 PM
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.



Chat with your friends as soon as they come online. Get Rediff Bol at
Received on Fri Feb 16 2001 - 10:30:27 PST
Custom Search