[gmx-users] non-water solvent + gmx solvate
Alex
nedomacho at gmail.com
Tue May 28 06:39:08 CEST 2019
Hi Kevin,
Emailed to your address. Just to clarify, there is really only one
issue, which is that we have a particular input that is making us stick
with 2018. Once that's been figured out, I'll be able to enjoy the great
new functionality in solvate. ;)
Thanks,
Alex
On 5/27/2019 8:15 PM, Kevin Boyd wrote:
> Hi Alex,
>
> Thanks for the followup, I've caught up on your previous thread with
> Szilard. Please do provide me the usage files for both issues at my uconn
> address. I'll certainly follow up on the gmx solvate stuff to make sure it
> works properly in the newest versions (since I did the most recent work on
> the tool), and I'll check out the mdrun segfaults when I get a chance, and
> make a ticket for the core developers - segfaults should never happen, and
> if they do we should be able to blame an external library :) .
>
> Cheers,
>
> Kevin.
>
> On Mon, May 27, 2019 at 9:05 PM Alex <nedomacho at gmail.com> wrote:
>
>> Hi Kevin,
>>
>> I used insert-molecules for now to get acetonitrile where it needed to
>> be, so it isn't much of an issue at the moment. We do have a more
>> serious problem with upgrading to the latest version, and that is the
>> 2019 mdrun either freezing or segfaulting on a particular simulation,
>> entirely unrelated to acetonitrile. To be fair, the 2018 version we are
>> using also hiccups on this setup, but does so only temporarily (thinks
>> about its life choices for 4-5 minutes at CPU load much lower than
>> normal) and proceeds with the run normally. 2019 dies permanently. If I
>> read your message correctly, you'd like to look into that. If that is
>> the case, I can of course send the input privately. Should I use your
>> UConn email?
>>
>> That said, I must warn you that the 2019 build issued a bunch of errors
>> on our end (see
>>
>> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mail-archive.com%2Fgromacs.org_gmx-users%40maillist.sys.kth.se%2Fmsg37181.html&data=02%7C01%7Ckevin.boyd%40uconn.edu%7C2a3d10ca44f14971ddd008d6e30886c3%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636946023101628806&sdata=kZJXxGF%2B34PHGnCGCcge9I77YJ9%2Bepq8BLlbqDTk%2FQk%3D&reserved=0),
>>
>> but Szilard assured me that it wasn't much of an issue. Indeed, the
>> build worked fine with our "usual" simulations. This one experiencing
>> issues (minor with 2018 and catastrophic with 2019) is new and it this
>> setup isn't expected to go away.
>>
>> Thanks a lot.
>>
>> Alex
>>
>> On 5/27/2019 2:33 PM, Kevin Boyd wrote:
>>> Hi Alex,
>>>
>>> I just looked back, and the 2018.3 release contained the fixes to gmx
>>> solvate that I was thinking of. If you're stuck on 2018 for other
>> reasons,
>>> could you check to see if the problem persists in the most recent branch
>> of
>>> that release family? I hope whatever other issue you're working through
>>> wouldn't have been introduced between 2018.2 and 2018.5, as the minor
>>> releases only make conservative bug fix changes.
>>>
>>> If you don't want to go through the installation trouble, can you send me
>>> sample files that trigger the issue offline, so I can check it?
>>>
>>> Thanks,
>>>
>>> Kevin
>>>
>>> On Sun, May 26, 2019 at 12:56 PM Alex <nedomacho at gmail.com> wrote:
>>>
>>>> Hi Kevin,
>>>>
>>>> I'm using 2018.2 -- had to roll 2019 back because it segfaults on a
>>>> certain simulation setup (I posted earlier about that, got no
>>>> responses). Kind of a disappointing situation... I guess I will use
>>>> packmol or just script it with insert-molecules.
>>>>
>>>> Alex
>>>>
>>>> On 5/26/2019 8:31 AM, Kevin Boyd wrote:
>>>>> Hi,
>>>>>
>>>>> Which version are you using? As of 2019 gmx solvate should support
>>>> nonwater solvents and topology updating.
>>>>> If it’s not working with 2019, can you open up an issue on
>>>> redmine.gromacs.org and upload your use files? I can take a look.
>>>>> Thanks,
>>>>>
>>>>> Kevin
>>>>>
>>>>>> On May 26, 2019, at 9:44 AM, Jones de Andrade <jdandrade at iq.ufrgs.br>
>>>> wrote:
>>>>>> Hi.
>>>>>>
>>>>>> Have you tried the packmol software?
>>>>>>
>>>>>> Good luck,
>>>>>>
>>>>>> Jones
>>>>>> --
>>>>>> Jones de Andrade
>>>>>> (jdandrade at iq.ufrgs.br)
>>>>>> DFQ/IQ/UFRGS
>>>>>> Lattes:
>> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flattes.cnpq.br%2F6675936210583999&data=02%7C01%7Ckevin.boyd%40uconn.edu%7C2a3d10ca44f14971ddd008d6e30886c3%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636946023101628806&sdata=5bL3LaawhCHP7%2F8ifYEW%2BD9ULdGJUHy8Fz8Z0NMCt2c%3D&reserved=0
>>>>>> Orcid:
>> https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Forcid.org%2F0000-0003-3429-8119&data=02%7C01%7Ckevin.boyd%40uconn.edu%7C2a3d10ca44f14971ddd008d6e30886c3%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636946023101628806&sdata=RMJ5XPVtx3p2Gn25VJNMi2lggkgWztJapB4xTUGKI1Q%3D&reserved=0
>>>>>> Enviado pelo K-9 mail
>>>>>>
>>>>>> Em 26 de maio de 2019 04:22:58 BRT, Alex <nedomacho at gmail.com>
>>>> escreveu:
>>>>>>> Hi all,
>>>>>>>
>>>>>>> I have a custom model for acetonitrile, which works fine when filling
>>>>>>> up
>>>>>>> a box using insert-molecules. When trying to use gmx solvate starting
>>>>>>> from a non-empty box, the utility displays a promising "Generating
>>>>>>> solvent configuration" and proceeds into nothingness with 100% CPU
>>>>>>> load.
>>>>>>> Trying a range of -radius and -scale values does not help. The reason
>>>>>>> for using solvate is of course the automatic topology update and not
>>>>>>> having to specify the number of solvent molecules.
>>>>>>>
>>>>>>> Is there any hope or should solvate be abandoned for non-water? Yes,
>> I
>>>>>>> did google this, and didn't like what I found
>>>>>>> (
>> https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gromacs.org%2FDocumentation%2FHow-tos%2FNon-Water_Solvation&data=02%7C01%7Ckevin.boyd%40uconn.edu%7C2a3d10ca44f14971ddd008d6e30886c3%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636946023101628806&sdata=pSUW7JLnoRZCKIsgSu2ls%2Fb5%2Bmlt6iUFQr8cP6sCxVo%3D&reserved=0
>> ).
>>>> I
>>>>>>> wonder if anything has changed...
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Alex
>>>>>>>
>>>>>>> --
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