From: Fotis Baltoumas (fbaltoumas_at_biol.uoa.gr)
Date: Fri Jul 07 2017 - 02:22:06 CDT
Hello,
The observations mentioned in the tutorial about the area perl lipid
mostly applied to CHARMM27 (for which the tutorial was originally
written). In C36 POPC and other phospholipids were reparametrized to
solve these issues, meaning that you don't really need UseConstantArea
enabled (on the other hand, I would use UseConstantRatio=on to keep the
XY ratio stable).
Having said that, I should point out that you're kind of comparing
apples to oranges. You're using POPC (average area per lipid = 68.3 in
the liquid phase in C36 if I remember correctly) to reproduce
experimental measurements on DOPC.
I would suggest that you try building an actual DOPC membrane using some
service like CHARMM-GUI (http://charmm-gui.org/), which can generate
NAMD inputs. Also, take a look at the namd configuration files they will
generate - this will give you a view on how you should set your options
for simulations with charmm36 lipids, as well as what you should look
for in temperature and pressure control.
Hope this helps,
Fotis Baltoumas
On 07/07/2017 04:49, yousef nademi wrote:
> Dear all,
>
> I build POPC lipid bilayer with the dimension of 18*18 using Charmm36
> Forcefield and membrane builder plugin in VMD. the total number of
> lipid molecules generated in this stage is 921 lipid molecules which
> mean each leaflet has approximately 461 lipid molecules.
> the experimental value for area per lipid for DOPC lipid bilayer is
> 65.8 A^2 at 271K. I used following procedure to equilibrate the
> membrane at 1 bar and 310k.
> 1- I run NVT simulation by keeping everything fixed except lipid tail
> to create the fluid like structure as suggested in the
> membrane-protein tutorial.
> 2- then, I run NPT simulation with following configuration file.
> the temperature of my simulation was 310K that means I should have a
> less packed structure in my system in comparison with
> mentioned experimental value. to obtain the experimental value of 65.8
> (A^2) for my lipid bilayer, I need my area to be 3.03338 *10^4 (A^2).
> after 0.5 ns, I have 2.85*10^4 (A^2) area. after 1ns, it will go
> below 2.8*10^4 (A^2) area. my area keeps shrinking by time.
> should I stop the shrinking at nearest possible experimental value and
> continue my simulation at fixed area suing useConstantArea =yes or is
> it something wrong with my configuration file.
> the membrane tutorial stated that "Simulation of membrane bilayers
> have shown that the current CHARMM forcefield parameters do no
> reproduce the experimentally observed area per lipid over long MD
> trajectories. During the previous simulation steps, we let the are in
> the xy-plane fluctuate to permit packing of lipids against the
> protein. However, after good packing has been observed, one should
> keep the area in the xy-plane constant."
>
> Thank you in advance,
>
> Yousef Nademi
>
> PhD student, Chemical and Material Department, University of Alberta,
> Canada
>
>
> set fs 748000
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
> set X 183.0400047302246
> set Y 183.06000518798828
> set Z 79.99099731445313
> set CX 41.34382247924805
> set CY 42.519981384277344
> set CZ 0.03781001642346382
>
> set PX 192
> set PY 192
> set PZ 80
>
> structure ./ionized.psf
> coordinates ./ionized.pdb
> extendedsystem ./popc_melting_lipid_tail-02-498000.restart.xsc
> bincoordinates ./popc_melting_lipid_tail-02-498000.restart.coor
> binvelocities ./popc_melting_lipid_tail-02-498000.restart.vel
>
> #set consfileName ./restrain_ionized_exceptlipidtail.pdb
> set temperature 310
> set outputname popc_melting_lipid_tail-02-748000
>
> firsttimestep $fs
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters ./par_all36_prot_na_lipid_pei_heparin-Jan2016.prm
> #temperature 0
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12
> switching on ;# to be checked the result w or w/o switching
> switchdist 10
> pairlistdist 12
>
>
> # Integrator Parameters
> timestep 2.0 ;# 1fs/step
> rigidBonds all ;# needed for 2fs steps "'shake bonh' in CHARMM?"
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10 ;# 'inbfrq 10 in CHARMM?'
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 10 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
>
> # Periodic Boundary Conditions
> cellBasisVector1 $X 0. 0.
> cellBasisVector2 0. $Y 0.
> cellBasisVector3 0. 0 $Z
> cellOrigin $CX $CY $CZ
>
> wrapAll on
> wrapWater on
> wrapNearest off
>
> margin 3
>
> # PME (for full-system periodic electrostatics)
> if {1} {
> PME yes
> # PMEGridSpacing 1.0
> PMEGridSizeX $PX
> PMEGridSizeY $PY
> PMEGridSizeZ $PZ
> }
>
>
> # Constant Pressure Control (variable volume)
> if {1} {
> useGroupPressure yes ;# needed for rigidBonds
> useFlexibleCell yes ;# no for water box, yes for membranees
> useConstantArea no ;# no for water box, maybe for membrane
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 200.
> langevinPistonDecay 100.
> langevinPistonTemp $temperature
> }
>
>
> # Output
> outputName $outputname
> binaryoutput off
> restartfreq 1000 ;#1000 steps= every 2 ps
> dcdfreq 1000
> xstFreq 1000
> outputEnergies 50
> outputPressure 50
>
>
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
> if {0} {
> fixedAtoms on
> fixedAtomsForces on
> fixedAtomsFile $consfileName
> fixedAtomsCol B
> }
>
> tclforces on
> set waterCheckFreq 100
> set lipidCheckFreq 100
> set allatompdb ./ionized.pdb
> tclForcesScript keep_water_out.tcl
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> run 250000 ;# 0.5 ns
>
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