Re: System expands: CCL4 simulation; NPT(Langevin Piston)

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Tue Apr 28 2009 - 16:56:35 CDT

Satya,

First, can you clarify? Did you switch to using the Rmin/2 value and do a
"namd restart?" (It's not explicitly detailed that the config file supplied
is that of your final "doubled in size" run.) If so, have you already tried
starting from the initial coordinates and can you confirm that it doesn't
"double in size" when starting from the very initial coordinates.

C.

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078
On Tue, Apr 28, 2009 at 4:10 PM, satya work <satya.work_at_gmail.com> wrote:
> Dear NAMD users,
>
> I have been encountering a rather strange problem with a simple NPT
> simulation of CCL4 molecules.
>
> I have used OPLS parameters for the CCL4 simulation and had
> accidentally given Rmin values for C and Cl instead Rmin/2 in the
> parameter file. The system runs but does not reproduce the correct
> density.
>
> After realising the above mistake, I give the correct values LJ values
> of C & Cl (Rmin/2), and not changing any other simulation conditions,
> the system size doubles and stays put !!
>
> The initial coordinates of CCL4 are at rather low density, so this
> expansion of the box for the correct values of Rmin/2 is confusing me.
>
> The Configuration file is attached below:
> --------------------------------------------------------
> structure          ./ccl4_namd_0.5k.psf
> coordinates        ./ccl4_namd_0.5k.pdb
> set previous        CCL4-run1
> set current         CCL4-run1
> #bincoordinates     ./$previous.restart.coor
> #binvelocities      ./$previous.restart.vel
> #extendedSystem     ./$previous.restart.xsc
> set temperature     298
> set outputname     ./$current
>
> firsttimestep       0
>
>
> #############################################################
> ## SIMULATION PARAMETERS                                   ##
> #############################################################
>
> # Input
> paraTypeCharmm      on
> parameters          ./par_all27_ccl4_cholesterol_ethanol.prm
> temperature         $temperature
> #temperature         5
> #reassignFreq       1000
> #reassignTemp       5
> #reassignIncr       5
> #reassignHold       310.0
>
>
>
> # Force-Field Parameters
> exclude             scaled1-4
> 1-4scaling          1.0
> cutoff              12.
> switching           on
> switchdist          10.
> pairlistdist        15.0
> margin               4.0
>
>
> # Integrator Parameters
> # fullElectFrequency*timestep <=4.0
> # stable time steps:
> #       with rigidBonds=all: electro:6fs;short-rangeNB:2fs;bonded:2fs
> #       otherwise          :         2fs               2fs        1fs
> timestep            2.0  ;# 2fs/step
> rigidBonds          all  ;# Needed for 2fs steps
> useSettle           on
> nonbondedFreq       1
> fullElectFrequency  2
> stepspercycle       10
>
>
> # Constant Temperature Control
> langevin            off    ;# do langevin dynamics
> langevinDamping     5     ;# damping coefficient (gamma) of 5/ps
> langevinTemp        $temperature
> langevinHydrogen    off    ;# don't couple langevin bath to hydrogens
>
> #temperature coupling for temperature coupling
> tCouple             on
> tCoupleTemp         $temperature
>
>
> # Periodic Boundary Conditions
> # center of the periodic box; NOT ORIGIN!!!
> cellBasisVector1    102            0.       0.
> cellBasisVector2     0.           102       0.
> cellBasisVector3     0.           0.       102
> cellOrigin            0.          0.        0.
>
> wrapAll             on
>
>
> # PME (for full-system periodic electrostatics)
> # multiples of 2,3,5 & >=dimensions above
> PME                 yes
> PMEGridSizeX        120
> PMEGridSizeY        120
> PMEGridSizeZ        120
>
>
> # Constant Pressure Control (variable volume)
> useGroupPressure      yes ;# needed for rigidBonds
> useFlexibleCell       no
> useConstantArea       no
>
> langevinPiston        on
> langevinPistonTarget  1.01325 ;#  in bar -> 1 atm
> langevinPistonPeriod  100.
> langevinPistonDecay   50.
> langevinPistonTemp    $temperature
>
>
> # Output
> outputName          $outputname
>
> restartfreq         500     ;# 500steps = every 1ps
> dcdfreq             500
> xstFreq             500
> outputEnergies      500
> outputPressure      500
>
>
>
> #############################################################
> ## EXECUTION SCRIPT                                        ##
> #############################################################
>
> # Minimization
> minimize           1000
> reinitvels          $temperature
>
> run 1000000 ;#
>
>

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