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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