AMBER Archive (2008)

Subject: RE: AMBER: a question

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Sep 28 2008 - 23:56:00 CDT

Hi Adrien,

 

This really depends on what your solute actually looks like. Both commands
are fine here, one will give you a orthorhombic box while the other will
give you a truncate octahedron, they both tessellate in 3 dimensions so give
you a full periodic system. The difference is in how many solvent molecules
are taken to build the unit. If your molecule is long and narrow and you
don't expect it to rotate on the timescale of the simulation then a
orthorhombic box is more efficient in terms of the number of solvent
molecules required. If you solute is approximately spherical, however, then
a truncate octahedron is better. Take a look at tutorial B1 on
http://ambermd.org/tutorials/ since this gives an explanation of how a
truncated octahedron works.

 

Note, you may want to check if anybody has parameterized the solvents you
want to use - otherwise if you are using, say GAFF parameters, then you
should check that you get the expected density, radial distribution
functions etc.

 

Good luck,

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Adrien Delmont
Sent: Sunday, September 28, 2008 3:08 PM
To: amber_at_scripps.edu
Subject: AMBER: a question

 

Dear All,

 

I'm using Amber 9 v. I want to run a simulation with many n-alkane
molecules. And I want to learn that which command is more suitable
?solvatebox or solvateoct? in order to generate a 'simulation' box
containing lots of my own molecules for using alkanes simulations in Amber?
Could you give me some information about this ?

Many Thanks in advance

Adrien

 

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