AMBER Archive (2008)

Subject: RE: AMBER: a question

From: Ross Walker (
Date: Mon Sep 29 2008 - 09:41:54 CDT

Hi Oguz,


I'm not sure I follow what you mean by whether you should use solvatebox or
solvateoct? In my last email I said that there is no "right or wrong"
choice... It depends on what your solute looks like and is an efficiency
consideration, I.e. truncate octahedron is a way to reduce the number of
solute molecules for an approximately spherical solute.


As for adding the same number of solute molecules in two different
simulations, assuming you have a valid reason for wanting to do this, then
the simplest way is to solvate one of them and make a note of how many
solute molecules get added. Then load the other system into leap and
effectively do a decimal search approach on the buffer argument for the
solvatebox command. I.e.


mymol1 = copy mymol

solvatebox mymol1 solute 12.0


if this adds to many solutes then try


mymol2 = copy mymol

solvatebox mymol2 solute 10.0


and repeat until you end up with less than you need. Then try increasing it
a little bit:




mymol3 = copy mymol

solvatebox mymol3 solute 10.5




Good luck,



From: [] On Behalf Of
oguz gurbulak
Sent: Monday, September 29, 2008 2:55 AM
Subject: RE: AMBER: a question


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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