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/
>
>
>
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:36 CST