Re: Lipid_bilayer_area_per_lipid_problem_using_NPT_CharmmForcefield

From: yousef nademi (yousef.namd_at_gmail.com)
Date: Fri Jul 07 2017 - 17:50:40 CDT

Hello Fotis,

Thank you for your answer. I misspelled the name of lipid bilayer. I used
POPC and I want to simulate POPC. Everything I said was about POPC. About
the area per lipid, I don't want to reproduce the exaxt experimental area
per lipid but I want the result to be logical, I use 310 K that means my
area per lipid should at least be higher than the experimental value at 273
K ( 65.8 A^2 at 271K) and not smaller. Still, I don't know why my area
keeps shrinking when I do not use constantArea or constantRatio.
Cheers,
Yousef Nademi

On Fri, Jul 7, 2017 at 4:49 PM, yousef nademi <yousef.namd_at_gmail.com> wrote:

> Hello Fotis,
>
> Thank you for your answer. I misspelled the name of lipid bilayer. I used
> POPC and I want to simulate POPC. Everything I said was about POPC. About
> the area per lipid, I don't want to reproduce the exaxt experimental area
> per lipid but I want the result to be logical, I use 310 K that means my
> area per lipid should at least be higher than the experimental value at 273
> K ( 65.8 A^2 at 271K) and not smaller. Still, I don't know why my area
> keeps shrinking when I do not use constantArea or constantRatio.
> Cheers,
> Yousef Nademi
>
> On Fri, Jul 7, 2017 at 1:22 AM, Fotis Baltoumas <fbaltoumas_at_biol.uoa.gr>
> wrote:
>
>> 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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