[gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer
jmsstarlight at gmail.com
Tue Feb 14 08:52:14 CET 2012
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
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)
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
How I could solve it?
2012/2/14 James Starlight <jmsstarlight at gmail.com>
> 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 ) ?
> 2012/2/14 Mark Abraham <Mark.Abraham at anu.edu.au>
>> On 14/02/2012 4:57 PM, James Starlight wrote:
>>> 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
>>> 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.
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