Hi,
This behavior has been fixed in the GitHub version of cpptraj:
https://github.com/Amber-MD/cpptraj/pull/676
Thanks for the report.
-Dan
On Tue, Mar 5, 2019 at 8:41 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> 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 - 09:30:02 PST
