From: Jeffrey Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Wed Feb 09 2011 - 10:51:41 CST
You don't have enough water in the box to give a density of ~1.0g/cm^3.
In your simulation the water is condensing to form a drop. Solution =
calculate how many water molecules you need to give you a density of 1.0
g/cm^3 (given a particular box size) and build a system with that many
waters.
Jeff
ais_at_fh.huji.ac.il wrote:
> hi,
> i'm running an npt simulation with periodic boundary conditions.
> i notice that as the simulation advances, the water box collapses into
> a shape similar to a sphere.
> the current run is a restart over a 40ps minimization that i ran
> earlier on the system.
> in the minimization script i specified the periodic cell dimensions
> but in the restart run i didn't since i gave a restart xsc file.
> - could anyone suggest an explanation for this phenomenon & point out
> what i've done wrong?
> - could this be related to the 'periodic cell has become too small for
> original patch grid...' error message that i get?
>
> i attach my restart conf file below. thanks, Ai
>
> #############################################################
> ## JOB DESCRIPTION ##
> #############################################################
>
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure 02_04_1zgoa_ion.psf
> coordinates 02_04_1zgoa_ion.pdb
> outputName 10_1zgoa
>
> set temperature 310
>
> # Continuing a job from the restart files
> if {1} {
> set inputname 07_1zgoa
> binCoordinates $inputname.restart.coor
> binVelocities $inputname.restart.vel ;# remove the "temperature"
> entry if you use this!
> extendedSystem $inputname.xsc
> }
>
> firsttimestep 40000
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters par_all27_prot_lipid_ai.inp
>
> # NOTE: Do not set the initial velocity temperature if you
> # have also specified a .vel restart file!
> # temperature $temperature
>
>
> # Periodic Boundary conditions
> # NOTE: Do not set the periodic cell basis if you have also
> # specified an .xsc restart file!
> if {0} {
> cellBasisVector1 82.67 0. 0.
> cellBasisVector2 0. 88.12 0.
> cellBasisVector3 0. 0 92.44
> cellOrigin 19.00 -14.80 38.19
> }
> 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 1.0 ;# 1fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2 stepspercycle 10
>
>
> #PME (for full-system periodic electrostatics)
> if {1} {
> PME yes
> PMEGridSizeX 90
> PMEGridSizeY 90
> PMEGridSizeZ 96
> }
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen no ;# don't couple langevin bath to hydrogens
>
>
> # Constant Pressure Control (variable volume)
> if {1} {
> useGroupPressure yes ;# needed for 2fs steps
> useFlexibleCell no ;# no for water box, yes for membrane
> useConstantArea no ;# no for water box, yes for membrane
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 200.
> langevinPistonDecay 50.
> langevinPistonTemp $temperature
> }
>
>
> restartfreq 500 ;# 500steps = every 1ps
> dcdfreq 500
> xstFreq 500
> outputEnergies 100
> outputPressure 100
>
>
> # Fixed Atoms Constraint (set PDB beta-column to 1)
> if {0} {
> fixedAtoms on
> fixedAtomsFile myfixedatoms.pdb
> fixedAtomsCol B
> }
>
>
> # IMD Settings (can view sim in VMD)
> if {0} {
> IMDon on
> IMDport 3000 ;# port number (enter it in VMD)
> IMDfreq 1 ;# send every 1 frame
> IMDwait no ;# wait for VMD to connect before running?
> }
>
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
> # Put here any custom parameters that are specific to
> # this job (e.g., SMD, TclForces, etc...)
>
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> if {0} {
> minimize 40000 ;#40 ps
> reinitvels $temperature
> }
>
> run 1000000 ;# 1000ps=1ns
>
>
>
>
>
-- ====================================================================== Jeffrey J. Potoff jpotoff_at_chem1.eng.wayne.edu Associate Professor Wayne State University Department of Chemical Engineering and Materials Science 5050 Anthony Wayne Dr Phone:(313)577-9357 Detroit, MI 48202 Fax: (313)578-5815 http://potoff1.eng.wayne.edu ======================================================================
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