[gmx-users] Re: Re:[gmx-users] box of methanol

[Anton Feenstra]

Erik Lindahl wrote:
> 
> As you probably noticed, this will be significantly slower since the
> atom density is now twice as high. Constraints or dummies won't help
> since the slow part is the nonbonded interaction calculation.

But they might help in the sense that it allows a larger time step
to be used to the same effective accuracy. I could think of a set-up
where only the C-O-H atoms are 'real' (i.e. have mass), and the C-O-H
angle is constrained (i.e. there is a constraints triangle C-O, O-H
and H-C). Then, from these three atoms you can construct the three
methyl hydrogens in a way similar to that for a dummified -NH3 or -CH3
group. 

Also see previous discussions on constraints & dummies on this list,
and look up the "Removing fast degrees of freedom" section in the
manual (Sec. 6.2, page 110).

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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