Re: Membranes

From: Erik Nordgren (nordgren_at_sas.upenn.edu)
Date: Thu Jul 21 2011 - 20:54:46 CDT

Hola Andrés,

Most of what you describe seems reasonable. But when you say that "the DPPC
bilayer lost its form", what exactly do you mean? Did it fall apart, or
change size or shape in some way? How so? And over what time scale did
this occur? Did the lipid bilayer remain "normal" in a control run, i.e.,
without adding the extra water?

Without knowing more info, it's hard to help. But given that your starting
point is a set of already-equilibrated lipid coordinates, one thing that
might be useful, I suppose, would be to run your lipid/water equilibration
at NVT (fixed MD box size) rather than letting the system dimensions
fluctuate with NPT dynamics.

-Erik

-- 
C. Erik Nordgren, Ph.D.
Department of Chemistry
University of Pennsylvania
On Tue, Jul 19, 2011 at 4:46 PM, Andres Morales N <
andresmoralesn2_at_hotmail.com> wrote:
>  Dear NAMD Users:
>
>
> It is the first time that I  work with phospholipid systems. I need to
> built a system with a DPPC bilayer, a peptide (ubicated outside the lipid
> bilayer) and water.
> I was looking for some tutorial about it, but I have only found tutorial
> about transmembranal proteins. Do yo know where I can find some documents
> about the protocol to work with this kind of systems (lipid
> bilayer+water+protein (ubicated outside the lipid bilayer)).
>
> For this reason I am trying with this procedure:
>
> -Minimize, heat to 300K, and equilibrate the lipid bilayer+water
> -Add the peptide to the system
> -Minimize, heat to 300K, and equilibrate the lipid bilayer+water+peptide
>
> I already got the pdf file for DPPC bilayer from LIPIDBANK. It is a
> pre-equilibrated system (bilayer+water). The problem is that the water layer
> is not wide enought to put the peptide there. So I tried to biuld a new
> system with a wider water layer, but when a run the equilibration of the
> system the DPPC bilayer lost its form. The scrip I use was:
>
>
>
>  structure          dppc_ws.psf
> coordinates        dppc_ws.pdb
> bincoordinates     dppc_cal300.coor
> binvelocities      dppc_cal300.vel
> set outputname     dppc_eq1ns
> firsttimestep      0
>
> #############################################################
> ## SIMULATION PARAMETERS                                   ##
> #############################################################
> # Input
> paraTypeCharmm     on
> parameters          par_all27_prot_lipid.prm
>
> # Force-Field Parameters
> exclude             scaled1-4
> 1-4scaling          1.0
> cutoff              12.
> switching           on
> switchdist          8.
> pairlistdist        13.5
> margin    0
> # Integrator Parameters
> timestep            1.0  ;# 1fs/step
> rigidBonds          all  ;# needed for 1fs steps
> nonbondedFreq       1
> fullElectFrequency  2
> stepspercycle       20
> #PME (for full-system periodic electrostatics)
> if {1} {
> PME                 yes
> PMEGridSizeX       80
> PMEGridSizeY       80
> PMEGridSizeZ       90
> }
> # 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    300
> }
> # Output
> outputName          $outputname
> dcdfreq             1000
> outputEnergies      100
>
> #############################################################
> ## EXTRA PARAMETERS                                        ##
> #############################################################
> # Boundary conditions
> extendedSystem      dppc_cal300.xsc
> wrapWater           on
>
> # Restrains
> fixedAtoms          on
> fixedAtomsCol       B
> fixedAtomsForces   on
>
> #############################################################
> ## EXECUTION SCRIPT                                        ##
> #############################################################
> # Equilibración
> run            2000000
>
>
>
> I do not know if this procedure is correct.
>
> Does anybody know how to solve it?
>
>
>
> I wait that someone can help me with this.
>
>
>
> Thanks for your help.
>
>
>
>
>
>
>  Hernán Andrés Morales Navarrete
>
> Biophysics and Molecular Modeling Group
> Physics Department
> Escuela Politécnica Nacional, Quito - Ecuador
> Ladrón de Guevara E11-253.
> Casilla 17-01-1253
> http://www.ciencias.epn.edu.ec/~biomod/
>
>
>

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