I've received the files and reproduced the error. The issue is that
you're running a SPAM pure water calculation on a trajectory that
contains solute (which I'm pretty sure you shouldn't do). The
'purewater` keyword is just so you can get an average "bulk" solvent
energy for use in a subsequent SPAM calculation.
That being said, the code shouldn't segfault - at worst it should exit
with an error. I'll work on a fix. Thanks for the report.
-Dan
On Mon, Mar 4, 2019 at 2:31 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> Can you send me off-list the topology and first 10 trajectory frames? Thanks.
>
> -Dan
>
> On Mon, Mar 4, 2019 at 12:15 PM Debarati DasGupta
> <debarati_dasgupta.hotmail.com> wrote:
> >
> > CPPTRAJ: Trajectory Analysis. V18.01
> > ___ ___ ___ ___
> > | \/ | \/ | \/ |
> > _|_/\_|_/\_|_/\_|_
> >
> > | Date/time: 03/04/19 12:13:49
> > | Available memory: 1.120 GB
> >
> > INPUT: Reading input from 'run.in'
> > [parm ./setup/ACN_IL1B_solvated.prmtop]
> > Reading './setup/ACN_IL1B_solvated.prmtop' as Amber Topology
> > Radius Set: modified Bondi radii (mbondi)
> > [trajin ./run_1/prod/ACN_IL1B_production4H.mdcrd]
> > Reading './run_1/prod/ACN_IL1B_production4H.mdcrd' as Amber NetCDF
> > [spam purewater name SPAM cut 12.0 out spampure.dat]
> > SPAM:
> > Calculating bulk value for pure solvent
> > Printing solvent energies to spampure.dat
> > Data set 'SPAM' index is water # * frame.
> > Using a 12.00 Angstrom non-bonded cutoff with shifted EEL.
> > #Citation: Cui, G.; Swails, J.M.; Manas, E.S.; "SPAM: A Simple Approach
> > # for Profiling Bound Water Molecules"
> > # J. Chem. Theory Comput., 2013, 9 (12), pp 5539รข5549.
> > [avg SPAM out spam.avg.dat name AVG]
> > AVERAGE: Calculating average of 1 data sets.
> > Data set base name 'AVG'
> > Output to to 'spam.avg.dat'
> > [go]
> > **************************************************************************************************************************************************************************
> > ---------- RUN BEGIN -------------------------------------------------
> >
> > PARAMETER FILES (1 total):
> > 0: ACN_IL1B_solvated.prmtop, 39605 atoms, 12325 res, box: Orthogonal, 12173 mol, 11955 solvent
> >
> > INPUT TRAJECTORIES (1 total):
> > 0: 'ACN_IL1B_production4H.mdcrd' is a NetCDF AMBER trajectory with coordinates, time, box, Parm ACN_IL1B_solvated.prmtop (Orthogonal box) (reading 1250 of 1250)
> > Coordinate processing will occur on 1250 frames.
> >
> > BEGIN TRAJECTORY PROCESSING:
> > .....................................................
> > ACTION SETUP FOR PARM 'ACN_IL1B_solvated.prmtop' (1 actions):
> > 0: [spam purewater name SPAM cut 12.0 out spampure.dat]
> > Found 11955 solvent residues [WAT]
> > Total Grid memory: 8.419 MB
> > TIME: Pair List Setup: 0.0186 s
> > Grid dimensions: 17 19 18 (5814 total).
> > ----- ACN_IL1B_production4H.mdcrd (1-1250, 1) -----
> > 0% *** Error in `cpptraj': munmap_chunk(): invalid pointer: 0x0000000002883f20 ***
> > ======= Backtrace: =========
> > /lib64/libc.so.6(+0x7f5d4)[0x7f3a7cdd05d4]
> > cpptraj[0x484ecc]
> > cpptraj[0x502b7c]
> > cpptraj[0x41058e]
> > cpptraj[0x5d2e0e]
> > cpptraj[0x5d3508]
> > cpptraj[0x71ab7f]
> > cpptraj[0x71b16b]
> > cpptraj[0x71f1c0]
> > cpptraj[0x72423f]
> > cpptraj[0x7269e9]
> > cpptraj[0x726e78]
> > cpptraj[0x40fd23]
> > /lib64/libc.so.6(__libc_start_main+0xf5)[0x7f3a7cd733d5]
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Mar 05 2019 - 06:00:03 PST
