[gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer
Mark Abraham
Mark.Abraham at anu.edu.au
Wed Feb 15 07:52:28 CET 2012
On 15/02/2012 4:45 PM, James Starlight wrote:
> 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.
Your system is dangerously small for those cut-offs if your initial
density is not correct for your model physics. Your y and z dimensions
only just contain a full cut-off sphere. You should also make sure you
are following the advice about choice of P-coupling algorithm in manual
3.4.9, and consider using a very small integration time step. I remain
unconvinced by this thread that you have generated a starting
configuration that does not have atomic clashes.
Mark
>
>
> James
>
>
> 2012/2/14 Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto: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/Pressure for
> background info.
>
> Mark
>
>
>>
>> James
>>
>>
>>
>> 2012/2/14 James Starlight <jmsstarlight at gmail.com
>> <mailto: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
>> <mailto: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
>> <mailto: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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