Re: question on membrane crushing

From: Himanshu Khandelia (hkhandel_at_dtc.umn.edu)
Date: Thu Mar 02 2006 - 08:57:12 CST

The charmm force field (also used in NAMD) has problems with flexible area
bilayer simulations. Cells either shrink or expand indefinetely. You will
need to use constant area or constant surface tension, with a flexible
cell in the direction of the bilayer normal. Strongly recommend the
following article, which talks about the flexible area problems.

Jensen, Mouritsen and Peters, Biophys J. 2004. 3556-3575

===================================================
Himanshu Khandelia

Doctoral Candidate,
Kaznessis Research,
Department of Chemical Engineering and Materials Science,
University of Minnesota

Mailing Address:

499, Walter Library,
117, Pleasant St. SE,
Minneapolis, MN 55455

Phone(o): 612-624-4945
===================================================

On Thu, 2 Mar 2006, Peter Freddolino wrote:

> Dear Longzhu,
>
> Generally when you're running a membrane it is a good idea to either
> turn on *useConstantArea or **useConstantRatio *to constrain the xy
> plane a bit. Also, may I ask why wrapnearest is on? Are you trying to do
> hexagonal cell simulations?
>
> Best,
> Peter
>
> Longzhu Shen wrote:
>
> >Dear All,
> >
> >I was trying simulating the POPE membrane with namd. I manually inserted a
> >peptide into the POPE model, ran minimization, heated the system, performed
> >position restrained md and free md. Everything went with along the
> >simulation. However, when I checked the trajectories with VMD, I found the
> >water on the two ends both moved toward the middle of the system. This made
> >the two leaves of the POPE further inserted to each other and lipid bilayer
> >severely crushed. The energy of the system looked stable during the whole
> >process with VDW slightly less than zero. I'd attache the configuration file
> >and wonder whether any kind guy could point out where I made mistakes. Many
> >thanks.
> >
> >sincerely,
> >
> >Longzhu Shen
> >
> >
> >------------------------------------------------------------------------
> >
> ># Input Force-Field Parameters
> >paraTypeCharmm on
> >parameters par_all27_prot_lipid.inp
> >
> >#
> >#molecules
> >
> >
> >set import ions_added
> >set export eqmd
> >
> >structure ${import}.psf
> >coordinates ${import}.pdb
> >#bincoordinates ${import}.coor
> >#binvelocities ${import}.vel
> >#extendedSystem ${import}.xsc
> >
> >set init_temp 0
> >set desired_temp 310
> >
> >#
> ># Output files & writing frequency for DCD
> ># and restart files
> >#
> >
> >outputname ${export}/eqmd
> >binaryoutput no
> >restartfreq 1000
> >binaryrestart yes
> >#dcdFile output/solvated_heat_out.dcd
> >
> >#
> ># Frequencies for logs and the xst file
> >#
> >outputEnergies 100
> >outputTiming 100
> >outputPressure 100
> >xstFreq 1000
> >dcdFreq 1000
> >
> >#
> ># Timestep & friends
> >#
> >
> >timestep 1.0 ;# 1fs/step
> >nonbondedFreq 1
> >rigidBonds all
> >rigidTolerance 0.00000001
> >fullElectFrequency 4
> >stepspercycle 20
> >
> >
> >#
> ># Simulation space partitioning
> >#
> >switching on
> >switchDist 10
> >cutoff 12
> >pairlistdist 16
> >
> >#
> ># Basic dynamics
> >#
> >temperature $init_temp
> >COMmotion no
> >dielectric 1.0
> >exclude scaled1-4
> >1-4scaling 1.0
> >
> >
> >#
> ># Particle Mesh Ewald parameters.
> >#
> >
> >PME yes
> >PMEGridSizeX 54
> >PMEGridSizeY 54
> >PMEGridSizeZ 75
> >
> >#
> ># Periodic boundary things
> >#
> >wrapWater on
> >wrapNearest on
> >wrapAll on
> >
> >margin 3
> >
> >
> >cellBasisVector1 52.45 0 0
> >cellBasisVector2 0 51.35 0
> >cellBasisVector3 0 0 74.67
> >cellOrigin -22.69 -22.61 -0.76
> >
> >#
> ># Fixed atoms for initial heating-up steps
> >#
> >fixedAtoms on
> >fixedAtomsForces on
> >fixedAtomsFile fix_backbone.pdb
> >fixedAtomsCol B
> >
> ># Restrained atoms for initial heating-up steps
> >#
> >constraints on
> >consRef restrain_ca.pdb
> >consKFile restrain_ca.pdb
> >consKCol B
> >
> >#
> ># Langevin dynamics parameters
> >#
> >langevin on
> >langevinDamping 1
> >langevinTemp $desired_temp #
> >langevinHydrogen on
> >
> >langevinPiston on
> >langevinPistonTarget 1.01325
> >langevinPistonPeriod 200
> >langevinPistonDecay 100
> >langevinPistonTemp $desired_temp #
> >
> >useGroupPressure yes
> >
> ># The actual minimisation and heating-up
> >
> ># run one step to get into scripting mode
> >minimize 0
> >
> ># turn off pressure control until later
> >langevinPiston off
> >
> ># minimize nonbackbone atoms
> >minimize 2500 ;#
> >output ${export}/min_fix
> >
> >#
> ># min all atoms
> >#
> >fixedAtoms off
> >minimize 2500 ;#
> >output ${export}/min_all
> >
> >#
> ># heat with Ps restrained
> >#
> >set temp $init_temp;
> >while { $temp <= $desired_temp } { ;#
> >langevinTemp $temp
> >run 10000 ;#
> >output ${export}/heating_Pr
> >set temp [expr $temp + 31]
> >}
> >
> >#
> ># equilibrate volume with Ps restrained
> >#
> >langevinPiston on
> >run 100000 ;#
> >output ${export}/equil_Pr
> >
> >#
> ># equilibrate volume without restraints
> >#
> >constraintScaling 0
> >run 500000 ;#
> >output ${export}/equil
> >
> >
>

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