Re: hi all

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Thu Jun 16 2011 - 07:29:53 CDT

By respammig the same message you are much more likely to annoy somebody
than to get an useful answer.
Restructure your question, check your spelling and your meaning.

Regards,
Ajasja

On Thu, Jun 16, 2011 at 14:16, kanchi subbarao rao <ksubbu85_at_gmail.com>wrote:

>
> hai to all ,
> I am running a simulation of dppc bilayer in NVT
> ensemble.but after equilibration i found the bilayer becomes disorder.
> I cont debug where I am doing mistake.
> and I am using
> * useFlexibleCell yes*
> * useConstantArea yes*
> * *
> is this the mean constant area per head group?
>
> shall anyone help me.
>
>
> thanks
> subbarao kanchi
>
>
> #############################################################
> ## JOB DESCRIPTION ##
> #############################################################
>
> # Min. and Eq. dppc_bilayer
> # embedded in POPC membrane, ions and water.
> # Melting lipid tails. PME, Constant Volume.
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure /home/subbu/delete/dppc-50ns-c27r-xplor.psf
> coordinates /home/subbu/delete/dppc-50ns-c27r.pdb
> outputName dppc_bilayermineq-01
>
> set temperature 250
>
> # Continuing a job from the restart files
> if {0} {
> set inputname dppc_bilayer
> binCoordinates $inputname.restart.coor
> binVelocities $inputname.restart.vel ;# remove the "temperature"
> entry if you use this!
> extendedSystem $inputname.restart.xsc
> }
>
> firsttimestep 0
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters
> /home/subbu/delete/parameters/par_all27_lipid_newfp2-dbond.prm
>
> # 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 {1} {
> cellBasisVector1 70. 0. 0.
> cellBasisVector2 0. 70. 0.
> cellBasisVector3 0. 0. 80.
> cellOrigin 0.2818959 0.00359906186 0.066067412
> }
> wrapWater on
> wrapAll on
> useFlexibleCell yes
> useConstantArea yes
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5
>
>
> # Integrator Parameters
> timestep 2.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 20
>
>
> #PME (for full-system periodic electrostatics)
> if {1} {
> PME yes
> PMEGridSizeX 70
> PMEGridSizeY 70
> PMEGridSizeZ 80
> }
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
>
> # Constant Pressure Control (variable volume)
> if {0} {
> useGroupPressure yes ;# needed for 2fs steps
> useFlexibleCell yes ;# 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 1000 ;# 1000steps = every 2ps
> dcdfreq 1000
> xstFreq 1000
> outputEnergies 50
> outputPressure 50
>
>
> # Fixed Atoms Constraint (set PDB beta-column to 1)
> if {0} {
> fixedAtoms on
> fixedAtomsFile /home/subbu/membrane-tutorial-files/kcsa_popcwi.fix
> fixedAtomsCol B
> fixedAtomsForces on
> }
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
> # Put here any custom parameters that are specific to
> # this job (e.g., SMD, TclForces, etc...)
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> if {1} {
> minimize 1000
> reinitvels $temperature
> }
> #Heating
> for {set TEMP 0} {$TEMP<=250} {incr TEMP 5} {
> langevinTemp $TEMP
> output md.$TEMP
> run 1000;#2ps
> }
>
> run 500000 ;# 1.0 ns
>
>

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