From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Mon Mar 13 2006 - 16:52:04 CST
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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