VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon Jul 27 2020 - 22:25:08 CDT

To get started looking at this, can you please let us know the version of
VMD that you are using? I am not able to reproduce the problem; simply
downloading the tutorial files and running the listed commands from the
tutorial for the M2 example works fine for me using VMD 1.9.3 (64 bit
linux).
Thanks,
Peter

On Mon, Jul 27, 2020 at 7:54 AM Manas Kohli <manaskohli1_at_gmail.com> wrote:

> 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.
>
>