From: Nicholas M Glykos (glykos_at_mbg.duth.gr)
Date: Wed Jun 30 2004 - 09:26:43 CDT
Dear All,
Three weeks ago I posted a question about the unexpected (to us) behaviour
of the dihedral energy term for one of our simulations. I have not
received any feedback as yet, so I thought that I could post again the
message this time including the corresponding NAMD script (included as
simple text at the end of this message) and asking even for negative
feedback (ie. if under similar conditions you have not observed anything
like the behaviour we are seeing).
Thanks,
Nicholas
____________________________ The problem ________________________________
We are running a 6 ns NPT simulation of a ~60000 atom system (using the
latest stable NAMD version) and we observe a very slow equilibration of
the dihedral energy term (or is it a drift ?). To make things easier to
visualise, I've put-up a picture showing the evolution of various terms
http://utopia.duth.gr/~glykos/MD_namd_list.png (88 KBytes)
For the run shown we use Nose-Hoover Langevin dynamics (320K, 1atm) with a
2 fs step, periodic boundary conditions, PME evaluation every four
timesteps, Shake, and (hopefully) suitable switching functions. The
structure of the protein has been and still is fairly stable.
Any insight as to why the dihedral energy term is taking so long to
equilibrate would be greatly appreciated,
__________________________ The NAMD script _____________________________
structure ionized.psf
coordinates heat_out.coor
velocities heat_out.vel
extendedSystem heat_out.xsc
parameters parallh22x.pro
parameters water+ions.par
restartname output/restart
restartfreq 1000
binaryrestart yes
outputEnergies 20
outputTiming 200
xstFreq 200
dcdFreq 200
wrapWater on
wrapNearest on
wrapAll on
timestep 2
rigidbonds all
nonBondedFreq 2
fullElectFrequency 4
stepsPerCycle 8
switching on
switchDist 10
cutoff 12
pairlistdist 13.5
Pme on
PmeGridsizeX 128
PmeGridsizeY 80
PmeGridsizeZ 64
exclude scaled1-4
1-4scaling 1.0
langevin on
langevinDamping 1
langevinTemp 320
langevinHydrogen on
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 200
langevinPistonDecay 500
langevinPistonTemp 320
useGroupPressure yes
binaryoutput off
outputname output/equi_out
firsttimestep 120000
run 3000000
--
Dr Nicholas M. Glykos, Department of Molecular
Biology and Genetics, Democritus University of Thrace,
Dimitras 19, 68100 Alexandroupolis, GREECE, Tel ++302551084036
Fax ++302551084037, http://origin.imbb.forth.gr/~glykos/
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