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

[Mark Abraham]

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 
> <mailto: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
>     <mailto: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
>         <mailto: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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