VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Wed Jul 29 2020 - 14:15:24 CDT

Thanks; I'm glad to hear that your channel is working.I'll file a bug
report on the vmd1.9.4 alpha issue; I am able to reproduce the problem in
VMD 1.9.4a43
Thanks,
Peter

On Wed, Jul 29, 2020 at 2:33 PM Manas Kohli <manaskohli1_at_gmail.com> wrote:

> Dear Peter,
>
> Thank you for your emails. The CG simulation now for my sodium channel
> seems to be holding up. I am attaching a tcl file with the output of
> running the tcl script '03a-solvate.tcl' for the POPC membrane patch. I am
> also attaching the psf and pdb files which could also make it a bit clearer
> as to what I mean in that the bead D3B is not assigned. Please let me know
> if you would require anything else and I will get back to you as soon as
> possible.
>
> Thanks and Best Regards,
> Manas
>
> On Wed, Jul 29, 2020 at 5:50 AM Peter Freddolino <petefred_at_umich.edu>
> wrote:
>
>> Glad to hear that things are working in VMD 1.9.3.
>> If a clean install of the latest VMD 1.9.4 alphas does not work, can you
>> please send the log/error files that I requested earlier? If there is a bug
>> floating around in the alpha builds of psfgen that would be very good to
>> know.
>> If you need a bigger coarse grained water box, you should just be able to
>> adapt the solvate command in 03a-solvate.tcl of the M2 example, perhaps
>> making the values for the -z and +z padding larger. Behind the scenes, that
>> script is using the nonstandard solvent box capability of vmd solvate, so
>> all normal capabilities of solvate apply.
>> Best,
>> Peter
>>
>> On Tue, Jul 28, 2020 at 8:21 PM Manas Kohli <manaskohli1_at_gmail.com>
>> wrote:
>>
>>> 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.
>>>>>>>
>>>>>>>