[gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

[James Starlight]

Justin,

I've built my system in accordance to the first way from your Biphgastic
system tutorial.

I've defined system with slight biger (  on 1 nm in each dimension)
dimensions that I needed and place maximym CCl4 molecules in that box by

genbox -ci ccl4.gro -nmol 900 -box  9.6 7.5 4 -o new_box.gro

So I've supposed that I've defined maximum density for such box. How else I
could specify starting density of my box?

2) I've tried use 1.4 VDV cutoff and crash of my system happened almost
alfter first 0.5 ns of simulation. By the way in the KALP tutorial I've
found Cutoff = 1.2. Why in that case you've used such uncommon values ?

James

2012/2/5 Justin A. Lemkul <jalemkul at vt.edu>

>
>
> James Starlight wrote:
>
>> Justin,
>>
>>
>>    Larger cutoffs would not only make the problem worse (read the error
>>    message carefully and consider the minimum image convention), but it
>>    would also potentially break the validity of the force field model.
>>     The vdW cutoff for Gromos96 should be 1.4 nm, not 0.9 nm, in any case.
>>
>>
>> This sounds controversially alitle :)
>>
>> Today I've tried such simulation with the 1.2 cutoffs and obtain the same
>> error on the 3rd ns ( density was 1.35 )
>>
>
> Still wrong.  Set rvdw = 1.4 and rcoulomb = 0.9 for Gromos96.  Don't play
> haphazardly with cutoffs.  Use what the force field dictates unless you can
> demonstrate that what you are doing is superior.  The original value of
> rcoulomb was 0.8 with reaction field, but 0.9 is fine in the case of PME.
>
>
>   From the error message I've understood that the problem was due to the
>> Z- box vector wich was decreased up to the 3 nm ( this is smaller rhan 2x
>> 1.2 of R_list cutoff ). So in accordance to that message I understood that
>> cutof must be > 1.5 in the case of my system didnt it?
>>
>>
> No, absolutely not.  You don't *want* the cutoffs to be equal to twice the
> box vector, they must always be *less* than this amount to avoid spurious
> PBC interactions due to minimum image violations.  Are you familiar with
> this concept and its implications?
>
> http://www.gromacs.org/**Documentation/Terminology/**
> Minimum_Image_Convention<http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention>
>
> You said in your first message:
>
>
> "2) Initially I've tried to use membrane mimicking dimensions 8.6   6.5
> 3.0 but during equilibration my box was shrinked to the 8.0 6.0 2.0"
>
> So your problem comes from the box shrinking to 2.0 nm in the z-dimension,
> which is less than twice your longest cutoff.  Your box is compressing in
> all directions, which means your initial configuration is too diffuse and
> the application of NPT conditions is squishing it together to arrive at the
> density the force field model predicts.  Build a system with an initial
> density closer to the target value.
>
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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