[gmx-users] non-water solvent + gmx solvate
Kevin Boyd
kevin.boyd at uconn.edu
Tue May 28 04:15:36 CEST 2019
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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