[gmx-users] rc or rlist in minimum image convention?

[Mark Abraham]

On 24/02/12, "Juliette N." <joojoojooon at gmail.com> wrote:

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> On 23 February 2012 20:07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
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> > On 24/02/2012 10:55 AM, Juliette N. wrote: 
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> > > Hi all,
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> > > My average size is 2.9 nm obtained from NPT under large pressure and now I intend  to increase rc to 1.4 and rlist to 1.65 nm. I am just worried about violating minimum image convention. 
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> > That probably violates the parametrization of your force field. 
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> Thanks Mark. You mean rc =1.4 for OPLS-AA is not appropriate? In the original OPLSAA:   Optimized Intermolecular Potential Functions for Liquid Hydrocarbons
> I see rc of 15 A has been used for alkanes which requires rlist of around 15+2.5+17.5 A ! Please comment why I am violating parametrization? Thanks.
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It is appropriate to use a set of .mdp parameters that most closely reproduce the parametrization conditions, or other conditions that have been shown to be effective. So if you were using rc<1.4 and now want to use rc=1.4, then it is likely that at least one of those choices is inappropriate. If 1.5nm was used in parameterization, then both the foregoing are probably unsuitable. The values for other rxxx parameters should be addressed in that work, and will depend on charge group size and electrostatics model.
 
Mark 
 

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> > > 1- My question is which of rc or rlist is important for minimum image convention?
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> > The larger one. See manual 3.2.2.
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> > > If its rlist then I think I have to make a bigger system.
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> > > 2- Will the simulation raise warning once half of the box size < rc or (rlist) ? I mean I want to make sure than over the course of simulation I am not breaching this rule.
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> > Under at least some circumstances such volume changes cause fatal errors. You can check for such after the fact with g_mindist -pi
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> Alright so I dont need to worry about it if simulation crashes under such conditions..
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> > > Thanks for your guidance, 
> > > J.
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