AMBER Archive (2008)

Subject: RE: AMBER: amber9 / difference of igb=0 and igb=6

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Jul 09 2008 - 15:54:54 CDT

Hi Arturas,

Igb=6 you should probably just consider as a debugging option for
generalized born.

Igb=1,2,5,7 does an implicit solvent (non-periodic) GB simulation. This uses
the routines in egb.f for the majority of the calculation.

Setting igb=6 will do a vacuum simulation but still using the routines in
egb.f - it just skips the GB parts. So you are getting a gas phase
simulation.

Effectively igb=6 is equivalent to igb=0, ntb=0 which does a vacuum
simulation as well but uses the code that forms part of the PME periodic
boundary side of the code tree.

In the event that you have an infinite cutoff (or a cutoff larger than the
largest extent of your system) then an igb=6 simulation should match an
igb=0, ntb=0 simulation. The difference occurs if you have a cut off since
the igb=0, ntb=0 (regular vacuum simulation) will make use of the standard
list builder used for direct space calculations in a PME simulation which
the igb=6 calculation will not use a list at all but will instead do the
cutoff calculation on every MD step. In theory they should end up
calculating the same thing as long as your system is well behaved such that
the pair list gets updated frequently enough.

In both cases there will be performance differences between the two options,
which is quicker will depend largely on the size of your system and the size
of the cutoff. For small cutoff and small systems igb=6 will probably be the
quicker option, while for larger cutoffs and larger systems igb=0,ntb=0 will
probably be quicker. All of this of course assumes that you are interested
in doing a vacuum simulation which is probably not what you want to be doing
with biological systems.

I hope this helps clarify things.
All the best
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Arturas Ziemys
> Sent: Wednesday, July 09, 2008 12:46 PM
> To: amber_at_scripps.edu
> Subject: AMBER: amber9 / difference of igb=0 and igb=6
>
> Hi,
>
> I am not sure I understand properly the difference of option of igb=0
> and igb=6 in AMBER 9: igb=0 - means no implicit solvation (no GB), igb=6
> - pure vacuum. I understand as both gives vacuum in non periodic
> systems. So what is the difference? Could anyone give a short comment?
>
> --
>
> Arturas Ziemys, PhD
> School of Health Information Sciences
> University of Texas Health Science Center at Houston
> 7000 Fannin, Suit 880
> Houston, TX 77030
> Phone: (713) 500-3975
> Fax: (713) 500-3929
>
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