[gmx-users] multi-component membrane simulation

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 12 17:48:11 CEST 2009

Stanislaw Bobritsky wrote:
> Hello everyone!
> It is given a lipid bilayer containing POPC (280 molecules), POPS (80) 
> and CHL(cholesterol, 40 molecules).
> When I try to minimize this system in vacuo (steepest descent), I can 
> see the following:
>         Warning: 1-4 interaction between 19 and 34 at distance 4.892
>         which is larger than the 1-4 table size 2.400 nm
> After that, of course, the system appears to be exploded.
> (all topologies were generated with ProDrug server)
> I tried to work with different component combinations. For example:
> 280 POPC:            Warning about 1-4 interaction, but system appears 
> to be alive. The 2nd minimization gives normal result with no warnings.
> 80 POPS:              The same.
> 40 CHL:                OK  
> 1POPC+1CHL:     OK
> 280POPC+80POPS:    FAIL (warnings like previous, system destruction)
> OK = no warnings, quick convergence.
> 280POPC+40CHL and 80POPS+40CHL boxes can be successfully minimized in 
> the same way. But if many POPC and POPS can be found in one box - the 
> resulting system is destroyed.
> How can it be fixed?

There is something unstable about the way you are preparing your system.  I know 
that's generic, but I don't know how you're putting everything together. 
Probably severe atomic overlap in the larger systems.  See here:


Also note that PRODRG topologies, at face value, are probably not correct.  They 
often (read: always!) require manual modification and validation before they 
should be considered trustworthy.  Lousy parameters might also cause problems.


> Thanks for help!
> Stanislaw Bobritsky,
> ChemBio Center, Taras Shevchenko National University, Kiev, Ukraine.
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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