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

[Juliette N.]

On 23 February 2012 21:18, Mark Abraham <mark.abraham at anu.edu.au> wrote:

> On 24/02/12, *"Juliette N." *<joojoojooon at gmail.com> wrote:
>
>
>
> On 23 February 2012 20:07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>
>>  On 24/02/2012 10:55 AM, Juliette N. wrote:
>>
>> Hi all,
>>
>> 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.
>>
>>
>> That probably violates the parametrization of your force field.
>>
>> 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.
>
>
> 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.
>

Thank you Mark. I was using rc =1.1 and just wanted to how much my results
vary by applying rc of 1.4 nm. I dont know the exact value that was used in
parametrization. I have just seen some previous works with cut offs around
these values. Is there anyway I can obtain plot of LJ potential versus
distance?

>
> Mark
>
>
>
>
>
>>
>>
>> 1- My question is which of rc or rlist is important for minimum image
>> convention?
>>
>>
>> The larger one. See manual 3.2.2.
>>
>>
>> If its rlist then I think I have to make a bigger system.
>>
>> 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.
>>
>>
>> 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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