Re: question on membrane crushing

From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Thu Mar 02 2006 - 08:32:34 CST

Hi Longzhu,

Even more generally, NpT simulations performed on systems that contain a
membrane should have the option useFlexibleCell activated
(useFlexibleCell yes) to account for the anisotropy of the system when
computing the pressure tensor. Then, you may or may not turn on
useConstantArea or useConstantRatio.

In addition, note that your time step of 1fs does not require rigidbonds
(unless you need it for a reason I cannot see from your conf file) and
that your pairListDist could be reduced to 14 or even less in order to
gain efficiency (see the classic reference Allen&Tildesley).

Finally, check that the distance between your periodic images in the Z
direction is at least 15A, which seems to be the case (20 or even 30A
would be better).

Regards,
Marcos

On Thu, 2 Mar 2006, Peter Freddolino wrote:

> Dear Longzhu,
>
> Generally when you're running a membrane it is a good idea to either turn on
> *useConstantArea or **useConstantRatio *to constrain the xy plane a bit.
> Also, may I ask why wrapnearest is on? Are you trying to do hexagonal cell
> simulations?
>
> Best,
> Peter
>
> 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
>>
>

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