[gmx-users] non-water solvent + gmx solvate
Kevin Boyd
kevin.boyd at uconn.edu
Mon May 27 22:34:17 CEST 2019
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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