[gmx-users] non-water solvent + gmx solvate
Alex
nedomacho at gmail.com
Tue May 28 03:04:50 CEST 2019
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://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg37181.html),
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:
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>>>> Orcid:
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>>>> 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%7Cab6bfb1c506341778cc408d6e1fb1e13%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C636944866006588215&sdata=lpDeWpl7JjWpTlUeCD2bvW1dvwJVT6Pwpi0LFAafNdw%3D&reserved=0).
>> I
>>>>> wonder if anything has changed...
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Alex
>>>>>
>>>>> --
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