VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue Jul 28 2020 - 15:01:58 CDT

Can you please redirect the stdout and stderr from those steps to files and
send them? Let's focus on the VMD1.9.3 machine. Have you ever installed a
1.9.4 alpha on that machine? The psfgen version bundled with vmd 1.9.3
should be 1.6.4 I believe, so I'm worried about where that message about
psfgen 2.0 is coming from.
Thanks,
Peter

On Tue, Jul 28, 2020 at 10:11 AM Manas Kohli <manaskohli1_at_gmail.com> wrote:

> 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.
>>>
>>>