VMD-L Mailing List

From: Manas Kohli (manaskohli1_at_gmail.com)
Date: Tue Jul 28 2020 - 19:21:30 CDT

Dear Peter,

Thank you for your email. It was actually an issue to do with VMD
versioning. The tutorial files are unable to run on VMD 1.9.4 or psfgen
2.0. I reinstalled VMD 1.9.3 and can now run the tutorial files properly. I
then tried to apply it to a new system to do with a voltage gated sodium
channel which was my initial goal for the CG simulation. When I ran the
simulation the minimisation worked initially but the simulation crashed due
to atoms moving too fast. When I examined the minimization structure and
dcd file it was apparent that the water box contracted too far in so parts
of the protein were sticking out which I think causes the simulation to
fail. My structure is rather large and I would require a larger coarse
grain water box than the one provided in the tutorial files. Could you
please help me with this? I think this would be the last issue before I
could run the CG simulation for my channel.

Thanks and Best Regards,
Manas

On Tue, Jul 28, 2020 at 9:02 PM Peter Freddolino <petefred_at_umich.edu> wrote:

> 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.
>>>>
>>>>