Temporarily awake and on cell. The "top of stack" here indicates that it is setting up the ewald charge grid when a memory acces error occurs, ergo if you minimize - a trivial step that cannot be minimized enough by critics - without ewald, you might get the job done. And maybe be able to run ewald md, forgetting this ever happened until you tell your grandchildren's old people minder bot. :-)
Or a different clue may result. I never worked on the ewald code, so can only guess so far.
Bill
<div>-------- Original message --------</div><div>From: Debarati DasGupta <debarati_dasgupta.hotmail.com> </div><div>Date:01/25/2019 8:00 AM (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject: Re: [AMBER] simple minimization error of a acetonitrile molecule in water (TIP3P water) </div><div>
</div>this is the pdb of acetonitrile I used.
________________________________
From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Sent: Friday, January 25, 2019 9:29 PM
To: amber.ambermd.org
Subject: [AMBER] simple minimization error of a acetonitrile molecule in water (TIP3P water)
sander -O -i min_all.in -o allmin.out -p C3N_WAT.prmtop -c C3N_WAT.inpcrd -r allmin.rst -x allmin.crd -ref C3N_WAT.inpcrd
Cannot understand at all what went wrong.
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x7FACEB01C6F7
#1 0x7FACEB01CD3E
#2 0x7FACEA52324F
#3 0x597E68 in __ew_recip_MOD_fill_charge_grid
#4 0x5989AC in __ew_recip_MOD_do_pmesh_kspace
#5 0x55DC6A in do_pme_recip_
#6 0x56091A in ewald_force_
#7 0x740673 in force_
#8 0x4EFCA9 in runmin_
#9 0x4DA58F in sander_
#10 0x4D13C5 in MAIN__ at multisander.F90:?
Segmentation fault (core dumped)
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Received on Fri Jan 25 2019 - 09:00:02 PST
