From: satya work (satya.work_at_gmail.com)
Date: Tue Apr 28 2009 - 23:44:02 CDT
Chris,
Sorry for the confusion.
I started a 'new' simulation from the initial coordinates after switching to
correct Rmin/2. The system still expands.
Satya
On Wed, Apr 29, 2009 at 3:26 AM, Chris Harrison <char_at_ks.uiuc.edu> wrote:
> 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 <http://www.ks.uiuc.edu/%7Echar>
> 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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