[gmx-users] Re: rvdw parameters (and other mdp stuff)

Anton Feenstra feenstra at chem.vu.nl
Thu Aug 15 09:07:21 CEST 2002

Graham Smith wrote:
> Just to make sure I've got this clear,
> with ffG43*,

seems OK. I hope you also read Berk Hess's message, where he
set some things right that I got wrong?

> (...and not rlist=rcoulomb=0.9, rvdw=1.4, which I started using a
> couple of months ago when I switched to PME. I got this by
> misunderstanding the manual (section 4.6.2) and mdp_opt.html; perhaps
> a note could be added to say that it applies only to ffgmx? Or is
> increasing rlist not as serious as decreasing it?)

We probably could.

> What parameters should I use with the new opls ff? Kaminski et al, J
> Phys Chem B 201 105 6474, state what cutoffs they've used only for
> their simulations of methanethiol and ethanethiol;
> unless I'm missing it, they don't mention the conditions for the
> simulations of peptides. They say
> intermolecular interactions were truncated at 11A, with the standard
> correction for the interactions beyond that radius [ref to 1984 JACS
> paper]. The ES interactions were quadratically feathered to zero over
> the last 0.5A before the cutoff.
> So if they're the same that would mean for ffopls protein simulations
> rlist                    = 1.1
> coulombtype              = PME
> rcoulomb-switch          = 1.05
> rcoulomb                 = 1.1

I would think their 'truncating' and 'feathering to zero' would imply:
rlist                    = 1.1
coulombtype              = Shift	; changed from 'PME'
rcoulomb-switch          = 0.5		; changed from '1.05'
rcoulomb                 = 1.1

But our 'shifted' potential might not 'feather' as theirs does...
When using 'shift', you'll also want vdwtype = shift .
Also, you would not be prohibited to set rlist to somewhat shorter than
1.1 (as per the explanation by Berk in the previous e-mail), e.g. to
rlist = 0.8 and nstlist = 5, which will improve your performance.

> Do I need to switch on DispCorr?

Don't know what they meant by 'standard corrections', maybe/also
reaction field (is also commonly used with the G43* ff's).

> While we're at it, I have always used a different temperature coupling
> group for each type of [ molecule ] in the .top, so I have e.g.
> This has propagated from an mdp I was given years ago (even though
> I've switched tc algorithm). But I've never really seen why it
> isn't always best just to tcoupl the whole system. I would think
> averages should be the same, but T-fluctuations will be reduced by
> somthing like sqrt(N_grp/N_system) with the groups coupled
> separately. Any comments?

The important thing here is the heat flow between different parts
of the system, which is related to the contact surface area of the
parts. For example, heat exchange will be abundant between water-
solvated ions and the water. But between a (largish) protein and
water it might be minimal. The other issue is heat-generation, 
which tends to be big(ger) for charged groups. So a (large) protein
will generate relative large amounts of heat, but not be able to
exchange that heat with the water. In that case, coupling the whole
system will lead to a correct average temperature of the system 
(obviously), but a hot protein (and a slightly cooler water).

You're probably right about the fluctuations, which is a reason
to choose your tcoupl groups as large as possible, with the
'heat-flow restriction' described above.

So, specifically, in your case I'd make a Protein group and
a Sol+Ions group... If you would have a ligand bound to the
protein, I'd add that to the protein group too. For a bilayer
system I'd imagine the bilayer would be a separate group,
but I have no experience with bilayer simulations...

(I hope Berk won't need to correct me on this one ;-)


 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "If You See Me Getting High, Knock Me Down"               |
|        | (Red Hot Chili Peppers)                                   |

More information about the gromacs.org_gmx-users mailing list