AMBER Archive (2008)

Subject: RE: AMBER: a question

From: oguz gurbulak (
Date: Mon Sep 29 2008 - 04:55:29 CDT

Dear Ross,
Thank you very much for your  advices. My aim is to evaluate thermophysical and structural properties of n- alkanes  and  binary mixtures  of n-alkanes. My molecules are n-heptan and n-tricosane. I positioned lots of n-heptan molecules into the simulation box. I used gaff force field and ‘solvatebox’ command as I atteched to the mail. Are my operations true or I should use solvateoct command? And also Ýs it possible to position the same numbers of n-heptan and n-tricosane  molecules ( binary mixtures of  n-heptan+n-tricosane   )  into the same simulation box?
Thanks in advance

--- On Sun, 9/28/08, Ross Walker <> wrote:

From: Ross Walker <>
Subject: RE: AMBER: a question
Date: Sunday, September 28, 2008, 11:56 PM

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 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,

From: [] On Behalf Of Adrien Delmont
Sent: Sunday, September 28, 2008 3:08 PM
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
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