Du Jiangfeng (BIOCH) wrote:
Dear Gro users, We created an all-atom system with 512 DPPCs by the method
which was suggested by Justin (genconf -f 128.gro -o 512.gro -nbox 2 2 1) and
a CG system with 512 DSPCs by using Martini self assembly tutorial. We do get
nice bilayers, however after minimization, the systems break apart. Also, if
Please define what "break apart" means - does the system explode, or do the
molecules simply split across PBC?
we add ions into the system, it also breaks apart. Our question is: What
Simply by adding ions? Or by doing EM afterwards?
causes the membrane to break apart during the minimization process? does it
mean that 512 lipids' system is not stable or is it a minimization method
problem? By the way, the minimization of a 128 lipids system has no problem.
Then maybe there is some clash in the system, although I'd be surprised if this
was the case. Assembling what essentially amount to periodic replicates via
genconf should be a robust procedure. If your EM is indeed blowing up, then the
log file (or screen output) should indicate where the high forces are. If
that's the case, check the structure in your favorite visualization program and
see what's wrong in that location.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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