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

[James Starlight]

This also was solved by the some extra minimisation steps.


I've forced with another problem :D

During npt equilibration my system have slightly expanded so my desired
volume and density were perturbed.

I've noticed the below options in npt wich could help me

ref_p        = 1 1
compressibility = 4.5e-5

 i'm using this compressibility value   because I'm modelling the
lipid-like environment so I think that I must increase pressure.  Could you
remind me the dependence of pressure from density and volume for liquids ?
:)

James



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

> 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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>
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