VMD-L Mailing List

From: Manas Kohli (manaskohli1_at_gmail.com)
Date: Mon Jul 27 2020 - 04:57:59 CDT

Dear all,

I have been having troubles running a CG simulation for the examples
provided for the residue based CG tutorial. The initial lipoprotein example
works fine but for the M2 channel and POPC membrane patch I am unable to
run them. Specifically the issue seems to lie with coarse graining the POPC
lipid itself to do with the D3B bead. psfgen can't seem to assign an atom
or coordinates for this bead and as a result it sits at position 0. This
then results in the following error message when running the simulation:

ERROR: Atom 1853 velocity is 4.59989e+15 1.18741e+14 7.46308e+13 (limit is
1200, atom 81 of 84 on patch 47 pe 0)
ERROR: Atom 1879 velocity is 3.4509e+15 -3.417e+15 1.32714e+13 (limit is
1200, atom 82 of 84 on patch 47 pe 0)
ERROR: Atom 1892 velocity is -8.05079e+15 3.29826e+15 -8.79022e+13 (limit
is 1200, atom 83 of 84 on patch 47 pe 0)
ERROR: Atoms moving too fast; simulation has become unstable (3 atoms on
patch 47 pe 0).
Warning: Low global exclusion count! (1536 vs 1752) System unstable or
pairlistdist or cutoff too small.
ERROR: Exiting prematurely; see error messages above.

Any other membrane protein embedded in POPC seems to fail because of the
same reason. I'm wondering how exactly to solve this issue with POPC for CG
simulations.