[gmx-users] Re: Npt equilibration of the membrane-mimicking CCl4 layer
Thomas Schlesier
schlesi at uni-mainz.de
Thu Feb 16 14:35:18 CET 2012
AFAIK vdwradii.dat is only used for *genbox*. For the actual simulation
the force field paramters of CCl4 will be used.
One thing which you could check is what is the compressibility of CCl4
(the value you use reminds me as that of water) and try with this. I do
not know if the is a protocol for what to do if you have an biphasic
system with different compressibilities. But this is only an idea, do
not if it would solve the problem.
greetings
thomas
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.
> >gmx-users Digest, Vol 94, Issue 95
> > 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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