Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer
James Starlight
jmsstarlight at gmail.com
Wed Feb 15 15:45:45 CET 2012
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 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 :)
Could you advise me another p_coup algorithm for my Ccl4 system?
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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