Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer
James Starlight
jmsstarlight at gmail.com
Fri Feb 17 06:46:34 CET 2012
So my problem still is
1) During npt without peptide my Ccl4 system expan rapidly in X-dimension.
That produce error on 2nd ns of equilibration
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.
2) During npt with peptide my system expan rapidly in Z direction ( along
that axe my peptide is oriented) So as concequence I've obtained the same
error.
Possible sollution wich I've found in litterature
1) To fix one dimension of my PB. How I could fix the X dimension of my box
during npt phace of pure Ccl4 and allow only change in 2 other dimensions ?
2) I have not found radius for Cl for Gromos56 ff.
Is this possible to decrease that value during npt phase to obtain system
with desired hight density? What value should I use?
James
2012/2/16 James Starlight <jmsstarlight at gmail.com>
> Mark,
>
> I'm using exact all parameters wich I found in different experimental work.
>
> By the way reducing of integration step to 1fs provide me with better
> equilibration of the Ccl4 system ( I've being obtained stabile system
> during 3 ns)
>
> but I had a problems during ntp equilibration when I inserted test peptide
> into that pre-equilibrated Ccl4 system and made two surrounded layer of
> water. My system was quickly eqxanded on Z-dimension and slightly shrinked
> on X.
>
> I think that such problem could be due to some problems with the vdw
> radius value for CCl4. E.g I didnt find this value in the vdwradii.dat file.
>
>
> James
>
>
> 2012/2/16 Mark Abraham <Mark.Abraham at anu.edu.au>
>
>> 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>
>> 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>
>>
>>
>> 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>
>>
>>> 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>
>>>
>>>> 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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>>
>>
>>
>>
>>
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>
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