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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