[gmx-users] POPC Bilayer box

[Simon Wang]

Thanks David:

I tried anisotropic low pressure at either 0.1 bar or 0.5 bar but the water 
layer was still squeezed from the corner of the box. I also tried NVT and 
the same thing happpened. Please give me more input. Following is the mdp 
file I used:

cpp                 =  /lib/cpp
define              =  -DPOSRES_LIPID   -DFLEX_SPC
integrator         =  md
dt                   =  0.002
nsteps             =  25000
nstcomm          =  1
;       Output control
nstxout             =  500.0
nstvout             =  500.0
nstlog               =  500.0
nstenergy           =  500.0
energygrps          =  POPC             SOL
;       Neighbor searching
nstlist                =  10
ns_type             =  grid
pbc                   =  xyz
;       Electrostatics and VdW
coulombtype       =  PME
rlist                    =  0.9
rcoulomb            =  0.9
rvdw                 =  1.2
fourierspacing      =  0.12
pme_order          =  6
ewald_rtol          =  1e-5
optimize_fft        =  yes
;       Temperature coupling
Tcoupl              =  berendsen
tc_grps             =  POPC           SOL
tau_t                =  0.1              0.1
ref_t                =  310              310
;       Pressure coupling
Pcoupl              =  berendsen
pcoupltype        =  anisotropic
tau_p               =  10.0    10.0    10.0     0       0       0
compressibility    =  4.5e-5   4.5e-5  4.5e-5  0       0       0
ref_p                =  0.1      0.1     0.1     0       0       0
;       Velocity generation
gen_vel             =  yes
gen_temp          =  310
gen_seed           =  173529
;       Bonds
constraints         =  all-bonds
constraint_algorithm =  lincs
unconstrained_start =  no
lincs_order         =  4
lincs_iter            =  1
lincs_warnangle   =  30

>On Mon, 2004-04-12 at 20:23, Simon Wang wrote:
> > Hello, David:
> >
> > I used either
> > 'genconf -f popc.gro -o popc4n.gro -nbox 2 2 1'
> > or 'genconf -f popc.gro -o popc4n.gro -trj popc200ps.trr -nbox 2 2 1'
> >
> > The version I used is GMX3.2.1. Please let me know if I missed anything 
>or
> > there is better way to scale the box size. Thanks a lot.
> >
>What you're doing is not scaling but increasing the system size by four.
>You could also have kept the water, I don't really get why you replaced
>it, but it might well be that you have a low pressure to start with
>because genbox did not fill all the holes...
>
>So if you use anisotropic slow pressure scaling everything should be
>fine. How is the density incorrect?
>
> > Simon
> >
> > >From: David <spoel at xray.bmc.uu.se>
> > >Reply-To: gmx-users at gromacs.org
> > >To: gmx-users at gromacs.org
> > >Subject: Re: [gmx-users] POPC Bilayer box
> > >Date: Mon, 12 Apr 2004 07:45:55 +0200
> > >
> > >On Mon, 2004-04-12 at 08:21, Simon Wang wrote:
> > > > Dear gmx-users,
> > > >
> > > > I started from Peter's popc128a.pdb and extended the z dimension and
> > >readded
> > > > water. The system was stable in 200ps w/ PME. Then I scale the box 
>size
> > >to a
> > > > larger one by genconf. The new system was fully minimized and run 
>50ps
> > >w/
> > > > pr. on the lipid. During the simulation, however, the waters at the
> > >corner
> > > > of the box began to move to the middle and the density was 
>incorrect.
> > >Please
> > > > enlighten me the reason for this and the possible solutions.
> > > >
> > >more details please, what did you do with genconf?
> > >
> > > > Thanks in advance,
> > > >
> > > > Simon

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