From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Nov 05 2015 - 10:21:42 CST
Hello:
I am getting troubles in converting (for a special ion) good oplsaa vdw
params to charmm. That is, rdf shows the expected octahedral solvation by
TIP3P water on MD for the ion in water, however the metal-O distances are
by some 20% too large (namd2.10 under following settings:
# temperature control
# temperature 300
langevin on
langevinTemp 300
langevinDamping 5
langevinHydrogen off
# constant pressure control
useGroupPressure yes
useFlexibleCell no
UseConstantArea no
useConstantRatio no
LangevinPiston on
LangevinPistonTarget 1.01325
LangevinPistonPeriod 200
LangevinPistonDecay 100
LangevinPistonTemp 300
# integrator
timestep 1.5 # 1.5 fs/step
nonbondedFreq 1 # nonbonded forces every step
fullElectFrequency 5 # PME only every five step
stepspercycle 20 # redo pairlist every 20 steps
# Approximations
# rigidBonds all ;# needed for 2fs/step
rigidBonds water
rigidTolerance 0.000001
exclude scaled1-4
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 13.5 # cutoff +3.5
margin 0
1-4scaling 1.0
PME yes
By adding
vdwGeometricSigma yes
minimization of the system does not go on (halting at the tcl request:
.................
Info: CREATING 68 COMPUTE OBJECTS
Info: useSync: 1 useProxySync: 0
Info: Startup phase 10 took 0.000324965 s, 118.027 MB of memory in use
Info: Startup phase 11 took 3.60012e-05 s, 118.027 MB of memory in use
Info: Startup phase 12 took 3.69549e-05 s, 118.156 MB of memory in use
Info: Finished startup at 0.0427089 s, 118.156 MB of memory in use
TCL: Running for 1000 steps
which is not surprising because there are also normal charmm params for
TIP3P water.
Thanks for advice about oplsaa -> charmm params conversion
francesco pietra
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