Re: RMSD increases after restarts, decreases at the end of run

From: yi wang (yiwang_at_ks.uiuc.edu)
Date: Fri Aug 25 2006 - 15:25:49 CDT

Hi,
      The config file looks normal to me, but just out of curiosity, how
was the RMSD calculated? did you compare with the same reference frame
for all of the trajectories, and then plot them on one figure?

       On Aug 24, 2006, at 5:16 PM, hodak_at_chips.ncsu.edu wrote:

> Hello,
>
> I am trying to equilibrate my system, I have done over 20 restarts and
> I
> have noticed strange thing: Almost always when I look at RMSD, RMSD
> increases at beginning of each restart, while it seems settled for over
> the last 10-20% of the run. This way it always seems that after one
> more
> restart RMSD will mostly oscillating, but the next restart brings it
> higher (at least initially). I am not sure if this is only coincidence
> or
> if my config file has problem and does not do proper restart or if
> this is
> a namd issue.
>
> I am attaching my config file, please look at it if it looks OK
> restart-wise:
>
>
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure ./full_wb.psf
> coordinates ./full_wb.pdb
> outputName ./restart25/full_wb_eq_restart25
>
> #set temperature 300
>
> # Continuing a job from the restart files
> binCoordinates ./restart24/full_wb_eq_restart24.restart.coor
> binVelocities ./restart24/full_wb_eq_restart24.restart.vel
> extendedSystem ./restart24/full_wb_eq_restart24.restart.xsc
>
>
> firsttimestep 72570
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters ../parameters/par_all27_prot_lipid.inp
>
> wrapWater on
> wrapAll on
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5
>
>
> # Integrator Parameters
> timestep 2.0
> rigidBonds all
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
>
> #PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 144
> PMEGridSizeY 128
> PMEGridSizeZ 128
>
>
>
> # Constant Temperature Control
> langevin on
> langevinDamping 5
> langevinTemp 300
> langevinHydrogen off
>
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes
> useFlexibleCell no
> useConstantArea no
>
> langevinPiston on
> langevinPistonTarget 1.01325
> langevinPistonPeriod 100.
> langevinPistonDecay 50.
> langevinPistonTemp 300
>
> #Output
>
>
> restartfreq 2000
> dcdfreq 2000
> xstFreq 2000
> outputEnergies 500
> outputPressure 500
>
>
>
>
>
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
>
>
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> #minimize 5000
> #reinitvels 300
>
>
> numsteps 433500
>
Thanks!

yi =]

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