[gmx-users] Semiisotropic pressure coupling
tarak karmakar
tarak20489 at gmail.com
Tue Feb 17 07:23:40 CET 2015
Hi All,
Just read the thread and got some new information. I'm currently simulating
a pure DPPC bilayer with charmm36 lipid parameters in gromacs-5.0.4.
In doing so, I got a lower area per lipid (~0.56 nm^2) compared to the
experimental one (~0.63nm^2). The trajectory has run for ~3-4 ns. I have
used the following NPT.mdp file with the new set of cut-off schemes and a
time step of 2 fs.
----------------------------------------------------------------------------------------------------------------------------------
title = NPT
integrator = md ; Algorithm ("md" = molecular dynamics [leap-frog
integrator]; "md-vv" = md using velocity verlet; sd = stochastic dynamics)
dt = 0.002 ; Time-step (ps)
nsteps = 5000000 ; Number of steps to run (0.002 * 500000 = 1 ns)
; Parameters controlling output writing
nstxout = 10000 ; Write coordinates to output .trr file
every 2 ps
nstvout = 10000 ; Write velocities to output .trr file every
2 ps
nstenergy = 10000 ; Write energies to output .edr file every 2 ps
nstlog = 1000 ; Write output to .log file every 2 ps
; 7.3.9 Neighbor Searching
nstlist = 10 ; [steps] freq to update neighbor
list
ns_type = grid ; method of updating neighbor list
pbc = xyz ; periodic boundary conditions in
all directions
cutoff-scheme = Verlet
vdwtype = cutoff
vdw-modifier = force-switch
rlist = 1.2
rvdw = 1.2
rvdw-switch = 1.0
; 7.3.10 Electrostatics
coulombtype = PME ; Particle-Mesh Ewald electrostatics
rcoulomb = 1.2 ; [nm] distance for Coulomb cut-off
fourierspacing = 0.12 ; [nm] grid spacing for FFT grid
when using PME
pme_order = 4 ; interpolation order for PME, 4 =
cubic
ewald_rtol = 1e-5 ; relative strength of
Ewald-shifted potential at rcoulomb
DispCorr = no
; Temperature coupling parameters
tcoupl = Nose-Hoover ; Modified Berendsen thermostat
using velocity rescaling
tc-grps = DPPC SOL_Ion ; Define groups to be coupled separately
to temperature bath
tau_t = 0.5 0.5 ; Group-wise coupling time constant (ps)
ref_t = 323 323 ; Group-wise reference temperature (K)
; Pressure coupling parameters
pcoupl = Parrinello-Rahman ; Pressure coupler used under NPT
conditions
pcoupltype = semiisotropic ; Isotropic scaling in the x-y
direction, independent of the z direction
tau_p = 5.0 ; Coupling time constant (ps)
ref_p = 1.0 1.0 ; Reference pressure for coupling,
x-y, z directions (bar)
compressibility = 4.5e-5 4.5e-5 ; Isothermal compressibility
(bar^-1)
; Initial Velocity Generation
gen_vel = no ; Velocity is read from the previous run
nstcomm = 1 ; COM removal frequency (steps)
comm_mode = Linear ; Remove COM translation (linear / angular /
no)
comm_grps = DPPC SOL_Ion ; COM removal relative to the specified
groups
; Parameters for treating bonded interactions
constraints = all-bonds ; Which bonds/angles to constrain (all-bonds
/ hbonds / none / all-angles / h-angles)
constraint_algorithm = LINCS ; Constraint algorithm (LINCS / SHAKE)
lincs_iter = 1 ; Number of iterations to correct for rotational
lengthening in LINCS (related to accuracy)
lincs_order = 4 ; Highest order in the expansion of the
constraint coupling matrix (related to accuracy)
continuation = no ; Whether a fresh start or a continuation from
a previous run (yes/no)
----------------------------------------------------------------------------------------------------------------------------------
Any comment on this?
Thanks and regards,
Tarak
On Tue, Feb 17, 2015 at 5:52 AM, shivangi nangia <shivangi.nangia at gmail.com>
wrote:
> Hello Justin,
>
> I have a follow up question.
>
> The non-bonded parameters you have pointed out to :
> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
>
> is valid if the system contains only lipid or it should be use with a
> system containing lipid and protein too.
>
> Thanks,
>
> sxn
>
>
> On Mon, Feb 16, 2015 at 2:10 PM, shivangi nangia <
> shivangi.nangia at gmail.com>
> wrote:
>
> > Thanks a lot Justin!!!
> >
> >
> >
> >
> >
> >
> > On Sun, Feb 15, 2015 at 1:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >>
> >> On 2/15/15 1:02 PM, shivangi nangia wrote:
> >>
> >>> Dear Justin,
> >>>
> >>> Thanks for the continuous help.
> >>>
> >>> Since I have done reverse CG, The CG POPC was equilibrated alone
> >>> anisotropically, The APL was fine there.
> >>> On reverse CG and NVT its still fine, it only after NPT it starts
> >>> dropping.
> >>>
> >>>
> >> Of course it's fine during NVT - the box can't change so the area is
> >> constant.
> >>
> >> I am calculating APL as (2*Lx*Ly)/(No. of Lipids).
> >>>
> >>>
> >> That's only valid for pure, symmetric membranes. You have a protein
> >> embedded in one leaflet, so this method is wrong.
> >>
> >> You mentioned to get gull force field from your site, is it here:
> >>>
> >>> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
> >>>
> >>>
> >> Yes, that's the right place.
> >>
> >> On unzipping this I see POPC is an .trp entry.
> >>>
> >>> If there is some other database, kindly point it out to me.
> >>>
> >>>
> >> What I'm telling you is to use those force field files to (1) verify
> that
> >> your POPC parameters are right (they should be) and (2) you'll have the
> >> right protein topology (there are different bonded parameters that will
> >> affect protein dynamics).
> >>
> >> Again, I must emphasize - troubleshooting the APL of this system with
> >> respect to the known APL of pure POPC is pointless. You have a protein
> >> that convolutes (and potentially changes) everything. If you want to
> >> simulate pure POPC to verify that things are fine, do that. But taking
> >> more time on any perceived discrepancies here is not productive.
> >>
> >>
> >> -Justin
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 629
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >> ==================================================
> >>
> >
> >
> --
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