From: suresh satpati (satpatisuresh_at_gmail.com)
Date: Tue Apr 09 2013 - 00:54:41 CDT
Dear Sir,
I m facing problem in running simulation for dna. i have got following
errors for which some solutions in NAMD mailing list is available (as to
check atom 474 velocity, it might be colliding with nearest atom). but i
don't know how to do that. plz let me know how to do that by using which
tool i have to do and how to do. plz forward some tutorial link or guidance
if possible.
amber on
ambercoor dna.inpcrd
parmfile dna.prmtop
temperature 0
outputEnergies 500
outputTiming 500
outputPressure 500
xstFreq 500
dcdFreq 500
restartfreq 50000
wrapAll on
wrapWater on
wrapNearest on
rigidBonds all
timestep 2
nonBondedFreq 1
fullElectFrequency 2
stepsPerCycle 20
switching on
switchDist 10.5
cutoff 12
pairlistdist 13.5
cellBasisVector1 64.688 00.000 00.000
cellBasisVector2 00.000 59.714 00.000
cellBasisVector3 00.000 00.000 59.789
cellOrigin 33.659 31.476 31.505
# the margin could be reduced once the cell is equilibrated
margin 5
Pme on
PmeGridsizeX 70
PmeGridsizeY 60
PmeGridsizeZ 60
exclude scaled1-4
1-4scaling 1.0
fixedAtoms on
fixedAtomsForces on
fixedAtomsFile dna_fix_backbone.pdb
fixedAtomsCol B
constraints on
consRef dna_restraint.pdb
consKFile dna_restraint.pdb
consKCol B
langevin on
langevinDamping 10
langevinTemp 310
langevinHydrogen no
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 200
langevinPistonDecay 100
langevinPistonTemp 310
useGroupPressure yes # smaller fluctuations
useFlexibleCell yes # allow dimensions to fluctuate
independently
useConstantRatio yes # fix shape in x-y plane
binaryoutput off
outputname dna_eq
# run one step to get into scripting mode
minimize 0
# turn off until later
langevinPiston off
# minimize nonbackbone atoms
minimize 40000
output min_fix
# min all atoms
fixedAtoms off
minimize 40000
output min_all
set temperature 10
#gradually heating
for {set i 10} {$i <= 310} {incr i 30} {
langevinTemp $i
run 10000
output heat_$i
}
# heat with CAs restrained
run 50000
output heat
# equilibrate volume with CAs restrained
langevinPiston on
run 50000
output equil_ca
# equilibrate volume without restraints 1000ps
constraintScaling 0
run 500000
ERROR: Constraint failure in RATTLE algorithm for atom 474!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
-- *Regards, Suresh Satpati*
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:06 CST