Hi Gustavo,
Thank you so much - this worked!
(i.e. I can now run sqm single points with the halorg-0-1 set, as well as
my original QM/MM minimisation with sander & the halorg-0-1 set)
Surprising it could be so simple...
BTW, you wrote "if it is *still* 700" - I did have all the updates
applied.
So I suppose it would be worth including this fix in the next AmberTools
update?
Best wishes,
Marc
On 4 February 2016 at 13:28, Gustavo Seabra <gustavo.seabra.gmail.com>
wrote:
> Hi Mark,
>
> Could you please check in your source code, in the file
>
> “$AMBERHOME/AmberTools/src/sqm/qm2_dftb_module.F90”,
>
> what is the value of the MAXTAB parameter, in line 24? If it is still 700,
> try changing it to 1500, and recompiling.
>
> —
> Gustavo Seabra.
>
>
>
> > Em 4 de fev de 2016, à(s) 09:37, Marc van der Kamp <
> marcvanderkamp.gmail.com> escreveu:
> >
> > Hi all,
> >
> > I encountered a problem when trying to run QM/MM minimisation with DFTB
> and
> > using *.skf files from the halorg-0-1 set. The error that occurs at the
> > very first step is:
> > QMMM SCC-DFTB: ***************************************************
> > QMMM SCC-DFTB: ERROR ON EWEVGE (Eigenvalue solver).
> > QMMM SCC-DFTB: ewevge: ier = 85 inner_scf_count= 1
> > QMMM SCC-DFTB: ***************************************************
> >
> > I know this error has been discussed before, but I haven't seen a
> 'general'
> > solution.
> >
> > I've been spending quite some time trying to narrow down where the error
> > comes from - and it appears to be related to the *.skf files (although
> > there may also be problems with how sqm reads them).
> > The amber-mailing list may therefore not be the appropriate forum, but
> I'm
> > hoping someone here may have some ideas - and at least it will be helpful
> > for others encountering the same problems.
> >
> > Using single point calculations in the latest version of sqm (version 14,
> > as included in AmberTools15 and also in AmberTools14), I've run the
> > following tests:
> >
> > 1) When using the halorg-0-1 set, CH3F runs fine. (I used
> > the /AmberTools/test/sqm/ch3f/ch3f.pm3.sp.in file, with PM3 replaced by
> > DFTB)
> >
> > 2) When using the halorg-0-1 set with my QM region that contains a -CH2F
> > group (and also O, N, S atoms), I get the Eigenvalue solver error
> >
> > 3) When using the halorg-0-1 set with my QM region where the -CH2F group
> is
> > replaced by -CH3, I ALSO get the Eigenvalue solver error
> >
> > 4) When using the default mio-0-1 set (so no halogens) with my QM region
> > where the -CH2F group is replaced by -CH3, I DON'T get the Eigenvalue
> > solver error
> >
> > At this point, it seems that the problem is with the halorg-0-1 *.skf
> files
> > that include O, N, or S.
> >
> > 5) When using the halorg-0-1 set and replacing S with O in my QM region
> > (and with the -CH2F group is replaced by -CH3), I ALSO get the Eigenvalue
> > solver error. (And still no error with the mio-0-1 set.)
> >
> > The problem is now appears to be narrowed down to the halorg-0-1 *.skf
> > files that include O & N (although those with S may also have a problem).
> > BUT:
> >
> > 6) When running with an input where F is replaced with H in the
> > ch3f.dftb.sp.in file, so creating ch4.dftb.sp.in (again no problem with
> the
> > mio-0-1 set), I get:
> > I get:
> >
> > Program received signal SIGSEGV: Segmentation fault - invalid memory
> > reference.
> >
> > Backtrace for this error:
> > #0 0x2AAAAACE6297
> > #1 0x2AAAAACE689E
> > #2 0x2AAAAB70869F
> > #3 0x2AAAAADA5D9D
> > #4 0x2AAAAADA1BD3
> > #5 0x2AAAAADA38B6
> > #6 0x49BE34 in gettab_
> > #7 0x4A22FF in qm2_dftb_load_params_
> > #8 0x45B380 in qm2_load_params_and_allocate_
> > #9 0x40F886 in sqm_energy_
> > #10 0x4117D7 in MAIN__ at sqm.F90:0
> > Segmentation fault
> >
> > (the output file is empty)
> > This appears to be a different issue, that I am rather lost on.
> >
> >
> > A further test shows that there is also a different problem with running
> > sqm with the halorg-0-1 *.skf files including O & N:
> >
> > 7) When running the $AMBERHOME/AmberTools/test/sqm/nma/nma.dftb.sp.in
> test
> > with the halorg-0-1 set (no error with the mio-0-1 set), I get:
> >
> > *** glibc detected *** sqm: free(): invalid pointer: 0x00002aaaabb47010
> ***
> > ======= Backtrace: =========
> > /lib64/libc.so.6(+0x75e66)[0x2aaaab74be66]
> > sqm[0x49d185]
> > sqm[0x40b079]
> > sqm[0x40b0cd]
> > /lib64/libc.so.6(__libc_start_main+0xfd)[0x2aaaab6f4d5d]
> > sqm[0x401e09]
> > ======= Memory map: ========
> > ...
> > ...
> > ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
> > [vsyscall]
> > Aborted
> >
> >
> > At this point, I am rather lost, apart from knowing that the halorg-0-1
> set
> > does not work in sqm (leads to the Eigenvalue solver problem) when having
> > O, N or S in a molecule, even though it does work with CH3F.
> > In addition, I get "Program received signal SIGSEGV: Segmentation fault -
> > invalid memory reference." errors when using the halorg-0-1 set in
> > molecules containing only C & H or S & F, tested with c2h2.dftb.sp.in
> and
> > h2s.dftb.sp.in, respectively)
> >
> > Sorry for the long email.
> > Any insight would be highly appreciated!
> >
> > --Marc
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Thu Feb 04 2016 - 06:30:03 PST
