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

James Starlight jmsstarlight at gmail.com
Thu Feb 16 13:16:14 CET 2012 

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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