Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer
Mark Abraham
Mark.Abraham at anu.edu.au
Wed Feb 15 22:20:51 CET 2012
On 16/02/2012 1:45 AM, James Starlight wrote:
> Mark,
>
> I've used that dimensions in accordance to some literature where the
> same membrane-mimicking simulation were performed.
>
> I've tried to rise cutoffs
Don't, that breaks your model physics and makes it even more likely you
will encounter problems with the system dimensions becoming too small
for the cut-off!
> and dicrease integration step but my system have been stil crashed
> during npt.
>
> I'm using
> pcoupl = Parrinello-Rahman
>
> wich I've found in the KALP tutorial because I have not found the same
> npt example file in the Biphastic tutorial :)
So you're following some other work and not copying their equilibration
protocol and/or model physics?
> Could you advise me another p_coup algorithm for my Ccl4 system?
There's only two choices available. Manual 3.4.9 specifically warns
against one of them for equilibration. What is there to say?
You should be sure to construct a simple case and get the model physics
validated. For the moment, forget about all the stuff where you were
struggling to insert more CCl4 into a box with CCl4 (probably creating a
far-from-equilibrium starting configuration). Don't try to learn to run
on stilts while shaving. Learn to shave, then to walk on stilts, then to
run, then start combining them.
Mark
>
> James
>
> ---------- Forwarded message ----------
> From: *Mark Abraham* <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>>
> Date: 2012/2/15
> Subject: Re: [gmx-users] Npt equilibration of the membrane-mimicking
> CCl4 layer
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
>
>
> 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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