[gmx-users] Re: Using CHARMM 36 for DPPC simulation

[Amit Choubey]

Hi Everyone,

I did another simulation where i found the the DPPC area per lipid is 0.61
nm^2 . Is this acceptable ?

I have seen issues like this on the mailing list before can one of the
experts give me some hints.

Amit

On Wed, Nov 9, 2011 at 12:24 PM, Amit Choubey <kgp.amit at gmail.com> wrote:

>
> 5Hello all,
>
> I am trying to use CHARMM 36 for DPPC membrane simulation. I did the
> following so far:
>
> 1. Download pdb file containing 128 DPPC molecules from
> http://www.charmm-gui.org/?doc=archive&lib=lipid_pure
>
> 2. I separated one lipid molecule from the obtained pdb file and used
> pdb2gmx -f 1dppc.gro -nochargegrp
>
> The top file obtained was converted to itp file by commenting few things
> out.
>
> 3. I looked at a file named dppc_n128.inp in the downloaded dppc bilayer
> from CHARMM GUI for the box length. I used editconf to convert the pdb to
> gro and manually inserted the box size in the gro file.
>
> 4. Created a system.top file which looks like
> #include "charmm36.ff/forcefield.itp"
> #include "lipid.itp"
> #include "charmm36.ff/tips3p.itp"
>
> [ system ]
> chol
>
> [ molecules ]
> DPPC 128
> SOL  3659
>
> 5. I used following mdp settings
>
> integrator = md ; leap-frog integrator
> nsteps = 20000000 ; 40 ns
> dt = 0.002 ; 2 fs
>
> ; Output control
> nstxout = 100000 ; save coordinates every 200 ps
> nstvout = 100000 ; save velocities every 200 ps
> nstenergy = 10000 ; save energies every 2 ps
> nstlog = 10000 ; update log file every 2 ps
>
> ; Neighborsearching
> ns_type = grid ; search neighboring grid cels
> nstlist = 10 ; 10 fs
> rlist = 1.0 ; short-range neighborlist cutoff (in nm)
> rlistlong = 1.4
> vdwtype = switch
> rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
> rvdw_switch = 0.8
>
> ; Electrostatics
> rcoulomb        = 1.0
> rcoulomb_switch = 0.0
> coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
> pme_order = 6 ; cubic interpolation
> fourierspacing = 0.15 ; grid spacing for FFT
>
> ; Temperature coupling is on
> tcoupl = Nose-Hoover ; More accurate thermostat
> tc-grps = DPPC SOL  ; two coupling groups - more accurate
> tau_t = 0.2 0.2 ; time constant, in ps
> ref_t = 323.15 323.15 ; reference temperature, one for each group, in K
>
> ; Pressure coupling is on
> pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
> pcoupltype = semiisotropic ; uniform scaling of x-y box vectors,
> independent z
> tau_p = 5.0 ; time constant, in ps
> ref_p = 1.0 1.0 ; reference pressure, x-y, z (in bar)
> compressibility = 4.5e-5 4.5e-5 ; isothermal compressibility, bar^-1
>
> ; Periodic boundary conditions
> pbc = xyz ; 3-D PBC
>
> ; Dispersion correction
> DispCorr = No ; account for cut-off vdW scheme
>
>
> ; Velocity generation
> gen_vel             =  yes
> gen_temp            =  200.0
> gen_seed            =  173529
>
> ; COM motion removal
> nstcomm         = 1
> comm-mode       = Linear
> comm-grps       = DPPC SOL
>
> ; Energy monitoring
> energygrps          =  DPPC SOL
>
> ; Bond parameters
> constraint_algorithm = lincs    ; holonomic constraints
> constraints     = hbonds     ; all bonds (even heavy atom-H bonds)
> constrained
> lincs_iter      = 1             ; accuracy of LINCS
> lincs_order     = 4             ; also related to accuracy
>
> The resulting simulation gave me an area per lipid =0.591 nm^2. This is
> not quite right. Can somebody suggest what else could i do it get close to
> the 0.63 nm^2 value.
>
> Also when i looked at trajectory file it seemed that the box length was
> not set up quite right because the downloaded pdb file looked ok with the
> membrane in the middle but at the next frame the membrane was at a totally
> different location. The leaflets were separated and the middle of the
> membrane was at the edge of the box.
>
> Also when i used pdb2gmx -nochargegrp on the downloaded file it created a
> gro file whose system size was
>    8.20170   8.64120   6.54740 in contrast to    6.40000   6.40000
> 6.38452 .
>
> Amit
>
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