From: arpita agarwal (arpita284_at_gmail.com)
Date: Thu Apr 21 2016 - 00:43:44 CDT
Dear All,
I am trying to run replica exchange for a protein with 8 replicas. Below is
my configuration file:-
timestep 1.0
structure protein.psf
coordinates protein.pdb
margin 5.0
stepspercycle 10
paratypecharmm on
parameters par_all27_prot_lipid.prm
exclude scaled1-4
1-4scaling 1.0
switching on
switchdist 10.0
cutoff 12.
pairlistdist 14.
langevin on
langevinDamping 5.0
langevinHydrogen off
rigidBonds all
nonbondedFreq 1
fullElectFrequency 2
wrapAll on
wrapWater on
wrapNearest on
dcdUnitCell yes
useGroupPressure yes
useFlexibleCell no
useConstantArea no
useConstantRatio no
langevinPiston no
#langevinPistonTarget 1.01325
#langevinPistonPeriod 100.0
#langevinPistonDecay 50.0
#xstFreq 100
#outputEnergies 100
#outputPressure 100
if {1} {
cellBasisVector1 x 0.0 0.0 ;# x-value for box
dimension
cellBasisVector2 0.0 y 0.0 ;# y-value for box
dimension
cellBasisVector3 0.0 0.0 z ;# z-value for box
dimension
cellOrigin a b c
PME yes
PMEGridSizeX x1
PMEGridSizeY x2
PMEGridSizeZ x3
PMEGridSpacing 1.0
}
When I am running this with periodic boundary conditions(PBC) then I am
getting the below error:-
*------- Partition 3 Processor 1 Exiting: Caught Signal ------Reason:
segmentation violationSuggestion: Try running with '++debug', or linking
with '-memory paranoid' (memory paranoid requires '+netpoll' at
runtime).Fatal error on Partition 3 PE 1> segmentation violation*
I think this is related to memory but there is no such issue being
observed.
When I am running the same configuration file without PBC, it's running
fine.
I am using the latest NAMD - NAMD_2.11_Linux-x86_64-netlrts.
Kindly suggest what could be the problem here.
Thank you.
Regards,
Arpita Srivastava
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