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

Mark Abraham Mark.Abraham at anu.edu.au
Wed Feb 15 07:52:28 CET 2012


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 
> <mailto: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
>>     <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
>>
>>                 -- 
>>                 gmx-users mailing list gmx-users at gromacs.org
>>                 <mailto:gmx-users at gromacs.org>
>>                 http://lists.gromacs.org/mailman/listinfo/gmx-users
>>                 Please search the archive at
>>                 http://www.gromacs.org/Support/Mailing_Lists/Search
>>                 before posting!
>>                 Please don't post (un)subscribe requests to the list.
>>                 Use the www interface or send it to
>>                 gmx-users-request at gromacs.org
>>                 <mailto:gmx-users-request at gromacs.org>.
>>                 Can't post? Read
>>                 http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>>
>>
>
>
>     --
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120215/d66d89e5/attachment.html>


More information about the gromacs.org_gmx-users mailing list