[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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