Re: question on membrane crushing

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Fri Mar 03 2006 - 14:49:42 CST

Hi Longzhu,

I've experienced the same problem, while building and equilibrating a
DMPC membrane. I was wondering if you found a solution? Or, did you try
applying constant area or constant surface tension, as some people
suggested? Did any of that help?

Thanks,

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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