Replica exchange

From: arpita agarwal (
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
cellBasisVector2 0.0 y 0.0 ;# y-value for box
cellBasisVector3 0.0 0.0 z ;# z-value for box
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

When I am running the same configuration file without PBC, it's running

I am using the latest NAMD - NAMD_2.11_Linux-x86_64-netlrts.

Kindly suggest what could be the problem here.

Thank you.

Arpita Srivastava

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