[gmx-users] multi-component membrane simulation
beavered at gmail.com
Mon Oct 12 17:34:58 CEST 2009
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
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
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?
Thanks for help!
ChemBio Center, Taras Shevchenko National University, Kiev, Ukraine.
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