Re: Re: Segmentation fault error with 'nan' pressure and energy

From: Sadegh Faramarzi Ganjabad (safaramarziganjabad_at_mix.wvu.edu)
Date: Wed May 31 2017 - 13:37:09 CDT

Hi Josh,

My simulation doesn't run that far to see those lines you mentioned. I
think runFEPmin section of fep.tcl allows a minimization step prior to FEP.
I tried that and it stops in the minimization step and gives the same 'nan'
error. So it gives the same error even when FEP/TI flag is on.

Also, there are some warnings in the output file

Warning: ALCH: SUSPICIOUS BONDS BETWEEN INITIAL AND FINAL GROUPS WERE FOUND
Info: ALCH: 6 DIHEDRALS LINKING INITIAL AND FINAL ATOMS DELETED

The first one is probably because I used extrabond to connect the initial
and final groups.

I'm putting my configuration file here.

Thanks,
Sadegh

# MD SETUP

timestep 2.0
numsteps 1

# FLEXIBLE CELL

useflexiblecell no

set temperature 310

# INPUT

structure all-ion-beta.psf
parameters par_all36m_prot.prm
parameters par_cph36_prot.prm
parameters par_all36_cgenff.prm
parameters par_all36_na.prm
parameters par_all36_carb.prm
parameters par_all36_lipid.prm
parameters toppar_water_ions_fixed.str
parameters retinal-pro.str
#parameters toppar_all36_lipid_model.str

paraTypeCharmm on
temperature $temperature

coordinates all-ion-beta.pdb
#bincoordinates equilibration.coor
#binvelocities equilibration.vel

#extendedSystem equilibration.xsc

# OUTPUT

outputenergies 100
outputtiming 100
outputpressure 100
binaryoutput yes

outputname forward-noshift-pr
restartname forward-noshift-pr
restartfreq 100
binaryrestart yes

XSTFreq 100

# PME

PME yes
PMETolerance 10e-6
PMEInterpOrder 4

PMEGridSpacing 1.0

# Periodic Boundary Conditions
if {1} {
cellBasisVector1 73.60 0.0 0.0
cellBasisVector2 0.0 73.60 0.0
cellBasisVector3 0.0 0 83.16
cellOrigin 0.030350102111697197 -0.059581365436315536
0.2382895052433014
}

# WRAP WATER FOR OUTPUT
wrapAll on

# CONSTANT-T

langevin on
langevinTemp 310.0
langevinDamping 1.0

# CONSTANT-P

# SPACE PARTITIONING

splitpatch hydrogen
hgroupcutoff 2.8
stepspercycle 20
margin 1.0

# CUT-OFFS

switching on
switchdist 10.0
cutoff 12.0
pairlistdist 12.0

# RESPA

fullElectFrequency 2
nonbondedFreq 1

# 1-4 NON-BONDED

exclude scaled1-4
1-4scaling 1.0

# COM

commotion no

# SHAKE

rigidbonds all
rigidtolerance 0.000001
rigiditerations 400

#############extra bonds

extraBonds on
extraBondsFile ref
########################

# FEP PARAMETERS

source ../tools/fep.tcl

alch on
alchType TI
alchFile all-ion-beta.pdb
alchCol B
alchOutFile forward-noshift-pr.fepout
alchOutFreq 10
alchBondDecouple on
alchBondLambdaEnd 1.0

alchVdwLambdaEnd 1.0
alchElecLambdaStart 0.0
alchVdWShiftCoeff 0.0
alchDecouple on

alchEquilSteps 100
set numSteps 500

runFEPmin 1.0 0.0 0.0625 20 20 310

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