VMD-L Mailing List

From: Manas Kohli (manaskohli1_at_gmail.com)
Date: Tue Jul 28 2020 - 09:11:29 CDT

Dear Peter,

Thank you for your reply. I have a linux computer with VMD 1.9.3 and
another freshly built computer with VMD 1.9.4 (new version of Ubuntu also)
and am getting the same error on both computers. When I execute the scripts
for either the POPC or M2 channel example, it initially runs until the fix
tcl script (typically until step 2). After that during the solvate step I
get:

version conflict for package "psfgen": have 2.0, need 1.4

and a similar error for solvate. I changed the version in the script so the
tcl script can execute but after this I end up getting the error for the
D3B bead I described before. For example:

ATOM 20 D3B POPCL 2 0.000 0.000 0.000 -1.00 0.00 L1

I'm also happy to send over any files with these so you could take a look
but I have changed nothing.

Thanks and Best Regards,
Manas

On Tue, Jul 28, 2020 at 4:25 AM Peter Freddolino <petefred_at_umich.edu> wrote:

> 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.
>>
>>