Re: question on membrane crushing

From: Himanshu Khandelia (hkhandel_at_dtc.umn.edu)
Date: Tue Mar 14 2006 - 12:05:13 CST

Arneh,

This is very very interesting. So you do not observe any systematic
contraction in your membrane in the NPT ensemble ? I do not recall any
simulation longer than 10 ns in CHARMM/NAMD where this has been achieved.

Could you please answer a few questions, which will really help us out:

1. how long are your simulations ?
2. what kind of boundary conditions are you using ?
3. what exactly do you mean by the NPT ensemble ? Are all the dimensions
of the unit cell flexible ? Is there a constant ratio in the x-y plane ?
Or is this an NPzAT ensemble, where the area is fixed, and the pressure
can fluctuate in the z-direction (the direction of the bilayer normal). It
would also help if you could show us a config file,

Thanks very much !

-Himanshu

===================================================
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 Mon, 13 Mar 2006, Arneh Babakhani wrote:

> Hi Longzhu,
>
> Ok, I think I know what's going on here, regarding this "crushing" effect.
>
> Through trial and error, I figured out that the most effect way to
> equilibrate my membrane (in my case, a DMPC one) is the following:
>
> 1. Build your membrane, using whatever template and script. I would
> make the thickness and area per lipid a little bit larger than your
> target thickness and area. So for instance, for DMPC (which normally has
> a thickness of 36-37 Angstroms), I originally constructed my membrane to
> have a thickness of 38.
>
> 2. Fix the tails. Minimize the headgroups
> 3. Fix the headgroups. Minimize the tails.
> 4. "Melt the tails". With the headgroups fixed, heatup your membrane
> to a high temp. I set mine to 450K, for about 20 ps. This step is
> crucial to randomize your tails.
> 5. Solvate your system
> 6. Minimize.
>
> Then perform constrained heating, and release the constraints gently. I
> think this is really crucial. There's several ways you can do this, I
> did the following:
> 7. Ran 20 ps heating to 310K, with HG/Tails/Water constrained with
> force constants of 10/5/2 kcal per mol, respectively.
> 8. Ran 20 ps heating to 310K, with HG/Tails/Water constrained with
> force constants of 5/2/0 kcal per mol, respectively.
> 9. Ran 20 ps heating to 310K, with HG/Tails/Water constrained with
> force constants of 2/0/0 kcal per mol, respectively.
> 10. Ran 20 ps heating to 310K, with HG/Tails/Water constrained with
> force constants of 0/0/0 kcal per mol, respectively. (In other words,
> all free, no constraints).
>
> Then I applied constant pressure and ran my production runs.
>
> Doing this, I found my membrane to equilibrate and retain more
> recognizable features. No crushing.
>
> Hope this helps,
>
> Arneh
>
> 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
> >
> >
>
>
> --
> ----------------------------
> Arneh Babakhani
> University of California at San Diego
> Physical Chemistry / Department of Chemistry & Biochemistry
> Laboratory of Prof. J. A. McCammon
> 9500 Gilman Drive MC 0365
> La Jolla, CA 92093-0365
>
> (619)895-6540
> (858)534-4974 (FAX)
>
> http://mccammon.ucsd.edu/~ababakha/
> ababakha_at_mccammon.ucsd.edu
>
>
>
>

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