Membranes

From: Andres Morales N (andresmoralesn2_at_hotmail.com)
Date: Tue Jul 19 2011 - 15:46:54 CDT

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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