AMBER Archive (2008)

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

From: Arturas Ziemys (arturas.ziemys_at_uth.tmc.edu)
Date: Wed Jul 09 2008 - 16:03:32 CDT

Thanks for solid answer! I was asking because I want to do a simulation
in "pure" vacuum, so asked differences of igb=1,6 options.
Arturas

Ross Walker wrote:
> 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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>
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-- 

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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