From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Mar 04 2011 - 15:50:13 CST
On Fri, Mar 4, 2011 at 4:07 PM, Davide Vanzo/FS/VCU <dvanzo_at_vcu.edu> wrote:
> Dear all,
dear davide,
> this is the first time I use Namd to run a MD simulation and I need to
> equilibrate a simple SPC/E water sample at 300K and 1atm with SHAKE. I
> started from a lattice of water molecules with SPC/E geometry at very low
> density in order to avoid superimpositions. The PBC cell is correctly
> centered and sized and the simulation ran without evidence of
> superimpositions. As you can see from the input script below I ran an NPT
it would have been much simple to take an already equilibrated water
restart, e.g. the one that ships with VMD for the solvate plugin. even
though it was built for a different water potential, this would have sped
up the process of equilibration significantly.
> simulation with temperature rescaling and langevin barostat. However the
> calculated pressure never reached the desired value, with strong
> oscillations (hundreds atm) around zero, and the compression stopped at
> densities higher than that expected for water.
> What is wrong?
probably nothing. you didn't say, how many water molecules you system
contains in total. the instantaneous pressure fluctuates a lot in dense
and not very compressible systems. you have to look at the long time
average. also, you didn't say what density you were comparing to what.
did you compute the average density of the last part of your MD? did
you compare to experimental water or SPC/E water (which is not exactly
the same!).
cheers,
axel.
>
>
>
> numsteps 100000
> timestep 1
> firsttimestep 0
> stepspercycle 20
>
> nonbondedFreq 1
> fullElectFrequency 1
>
> cutoff 10
> switching off
> switchdist 8
> pairlistdist 12
>
> exclude scaled1-4
> 1-4scaling 1
>
> rigidBonds all
> rigidTolerance 0.00000001
> rigidIterations 100
> rigidDieOnError on
>
> vdwGeometricSigma yes
>
> PME on
> PMETolerance 0.00001
> PMEInterpOrder 4
> PMEGridSpacing 1
>
> dielectric 1
>
> ZeroMomentum yes
>
> cellBasisVector1 68 0 0
> cellBasisVector2 0 68 0
> cellBasisVector3 0 0 68
> cellOrigin 34 34 34
>
> wrapAll off
>
> temperature 300
> COMmotion no
>
> rescaleTemp 300
> rescalefreq 5
>
> langevinPiston on
> langevinPistonTarget 1.01325
> langevinPistonTemp 300
> langevinPistonDecay 200
> langevinPistonPeriod 400
>
> useFlexibleCell no
> useGroupPressure yes
>
> coordinates water_5K.pdb
> structure water_5K.psf
> paratypeCharmm on
> parameters spce_water.par
>
> outputEnergies 50
>
> binaryoutput no
> outputname water_r1
>
> binaryrestart yes
> restartname water_r1_rst
> restartfreq 10000
>
> DCDfile water_r1.dcd
> DCDfreq 1000
>
> XSTfile water_r1.xst
> XSTfreq 1000
>
>
>
> This is my parameter file for SPC/E water
>
>
>
> BONDS
> OSP HSP 450.000 1.0000
> HSP HSP 0.000 1.6330
>
> ANGLES
> HSP OSP HSP 55.000 109.4700
>
> NONBOND
> HSP 0.000000 -0.000001 0.000000
> OSP 0.000000 -0.155350 1.582760
>
> END
>
>
>
> whether the topology file is
>
>
> 18 1
>
> MASS 1 HSP 1.00797 H
> MASS 2 OSP 15.99940 O
>
> DEFAULT FIRST NONE LAST NONE
>
> RESI SPE 0.0000
> GROUP
> ATOM O OSP -0.8476
> ATOM HA HSP 0.4238
> ATOM HB HSP 0.4238
> BOND O HA O HB HA HB
> ANGLE HA O HB
> DONOR HA O
> DONOR HB O
> ACCEPTOR O
> PATCHING FIRST NONE LAST NONE
> END
>
>
>
> Thank you to anyone could help me.
>
> Davide
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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