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

[Thomas Schlesier]

I assume that you energy minimisd the system, but still have atomic clashes?

One thing which helped me in a similar case, was a short simulation at 
low temperature with a really small timestep (about 3-5 magnitudes 
smaller than the normal timestep). With this the atoms which clashes 
move away from each other, but due to the very small timestep, they are 
not fast as rockets and shouldn't lead to an exploding system.
Then when most clashes are resolved you can continue with a normal 
equilibration.

Greetings
Thomas



 >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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