AMBER Archive (2009)

Subject: RE: [AMBER] Fw:how to select force field

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Mar 08 2009 - 12:52:56 CDT

Hi Nancy,

> I have one qustion ,I have created promtop and inpcrd files with
> xleap .But I am not sure whether the force field and solvent model are
> appropriate .My unit is carbon nanotubes,solvent is water ,I chosen ff99SB
> as force field in xleap.Maybe it is not correct ,i have read ambertools
> about force filed ,i can understand a little ,not much ,also I use
> (solvatebox)cubic water model ,I don not know solvatebox and solvateoct
> which is more suitable. can anybody give me some detailed explanation
> about the diffrences and usage of fore fields and solvent modals.

SolvateOct will give you a truncated octahedron water box. If your system is
long, like DNA for example or in your case a carbon nanotube and your expect
that your system will rotate on the timescale of the simulation then a
truncated octahedron can offer a more efficient water box since it has less
waters for a given rotation sphere to fit inside. If you carbon nanotube is
fixed in some way such that it won't rotate, or your simulations aren't long
enough for it to rotate then a rectangular box as solvatebox gives you
should be appropriate.

With regards to the force field this is a very subjective question and the
answer is very difficult. I would suggest doing a thorough literature search
to see who has done MD simulations of carbon nanotubes and what they used.
Has anyone used FF99SB for this before, has anyone tried to compare the
performance of different force fields? I would suspect that FF99SB would do
reasonably well but you need to realize that a carbon nanotube is well
outside of the design specs / training set for the force field which was
designed for simulating proteins. As long as you are aware of this then
things should be okay.

All the best
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber