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

[James Starlight]

It seems that I've fixed that problem by reduce vdv radii for Cl during
defining of my box

Eventually I've obtained box with the desired density
 than I've delete vdvradii.dat for my wor dir

by when I've launched equilibration I've oibtained

Fatal error:
Too many LINCS warnings (1598)
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file

I've never seen this before

I'm using 1.o cutoff for pme and 1.4 for vdv
my LINKS parameters are

; Bond parameters
continuation    = no        ; first dynamics run
constraint_algorithm = lincs    ; holonomic constraints
constraints    = all-bonds    ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter    = 1        ; accuracy of LINCS
lincs_order    = 4        ; also related to accuracy

How I could solve it?


James

2012/2/14 James Starlight <jmsstarlight at gmail.com>

> Mark,
>
> I've checked only density value
>
> with 500 molecules Ccl4 I have  density that is twisely less that I need (
> in accordance to the literature ). Also I've checked my box visually and
> found that the box is not properly tightly packed so I dont know why genbox
> didnt add some extra mollecules :(
>
> In other words I wounder to know if  there is any way to add some extra
> molecules to the pre defined box to make my system more tighly packed  ( to
> short distance between existing molecules and place new ones in the new
> space ) ?
>
> James
>
>
> 2012/2/14 Mark Abraham <Mark.Abraham at anu.edu.au>
>
>> On 14/02/2012 4:57 PM, James Starlight wrote:
>>
>>> Justin,
>>>
>>> Firstly I've created the box of desired size with only 500 molecules ( I
>>> need 1000)
>>>
>>> Than I've tried to add extra 200 molecules by means of Genbox
>>>
>>> genbox -cp super_box.gro -ci Ccl4.gro -nmol 200 -o new_solv.gro
>>>
>>> but no molecules have been added
>>> Added 0 molecules (out of 200 requested) of Cl4
>>>
>>
>> ... then there are no gaps large enough to insert your molecules. Either
>> make gaps, or check out genbox -h for advice on defining the radii.
>>
>>
>>
>>> also I've tried
>>>
>>> genbox -cp super_box.gro -cp Ccl4.gro -nmol 200 -o new_solv.gro
>>>
>>
>> Two -cp options is not what you want, and -nmol probably only works with
>> -ci.
>>
>>
>>
>>> but system were crashed with message
>>>
>>> Reading solute configuration
>>> God Rules Over Mankind, Animals, Cosmos and Such
>>> Containing 2500 atoms in 500 residues
>>> Initialising van der waals distances...
>>>
>>> WARNING: masses and atomic (Van der Waals) radii will be determined
>>>         based on residue and atom names. These numbers can deviate
>>>         from the correct mass and radius of the atom type.
>>>
>>> Reading solvent configuration
>>> "God Rules Over Mankind, Animals, Cosmos and Such"
>>> solvent configuration contains 5 atoms in 1 residues
>>>
>>>
>>> Is there any ways to add extra mollecules to the pre defined box ?
>>>
>>
>> Yes - but there has to be room for them.
>>
>> Mark
>>
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