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

[James Starlight]

Mark,


due to hight density the volume of my system have been slightly increased
and during NPT phase I've obtained error

Fatal error:
One of the box vectors has become shorter than twice the cut-off length or
box_yy-|box_zy| or box_zz has become smaller than the cut-off.

I'm using 0.9 for electrostatic and 1.4 for vdw cutofs and the dimensions
of my box was 6.5 3 3 on the initial step and 6.6 3 3.3 before crush :)

I want prevent such expansion of my system by increasing of pressure and/
or compressibility but I have not found exact sollution yet.


James


2012/2/14 Mark Abraham <Mark.Abraham at anu.edu.au>

>  On 14/02/2012 11:01 PM, James Starlight wrote:
>
> 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 ?
> :)
>
>
> Your forcefield, simulation cell contents and .mdp settings will determine
> the equilibrium density. Whether you need to do anything depends on whether
> you've made a statistically significant post-equilibration measurement of
> your average density. Haphazardly increasing the reference pressure for the
> coupling will reduce the volume, but now you are simulating at that
> pressure. See http://www.gromacs.org/Documentation/Terminology/Pressurefor background info.
>
> Mark
>
>
>
> 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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