[gmx-users] lower Area per lipid for DPPC with CHARMM36
tarak karmakar
tarak20489 at gmail.com
Tue Feb 17 07:09:37 CET 2015
Hi Justin,
Still there is some problem. In the short equilibration I've got the good
value of the Area per lipid. But now in the production run, it kept on
decreasing. Presently, the value is ~56 A^2. The following .mdp has been
used.
----------------------------------------------------------------------------------------------------------------------------------
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 suggestion would be helpful.
Thanks,
Tarak
On Mon, Feb 16, 2015 at 4:01 PM, tarak karmakar <tarak20489 at gmail.com>
wrote:
> Oh! Thanks. :)
> Sorry I should have checked it before running the simulation.
> Now, I'm getting APL ~62.5 A^2 which is pretty good compared to the expt.
>
>
>
> On Sun, Feb 15, 2015 at 6:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 2/15/15 7:39 AM, tarak karmakar wrote:
>>
>>> Dear All,
>>> All atom simulation of DPPC bilayer (128 lipids) is resulting a low area
>>> per lipid (sliding down from ~58 to ~54 in 4 ns NPT).
>>> I'm performing the simulation in gromacs-5.0.4 with the charmm36 force
>>> field parameters for the lipid molecules. The NPT.mdp is pasted bellow,
>>>
>>>
>> We've been discussing this exact topic in another thread for days...
>>
>> Your .mdp settings are wrong.
>>
>> http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM
>>
>> -Justin
>>
>>
>> ------------------------------------------------------------
>>> -------------------------------------
>>> title = NPT production for cxcr_WT
>>> ; Parameters describing the details of the NVT simulation protocol
>>> 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 = 10000 ; Write output to .log file every 2 ps
>>>
>>> ; Parameters describing neighbors searching and details about interaction
>>> calculations
>>> ns_type = grid ; Neighbor list search method (simple, grid)
>>> nstlist = 5 ; Neighbor list update frequency (after every
>>> given number of steps)
>>> rlist = 1.2 ; Neighbor list search cut-off distance (nm)
>>> rlistlong = 1.4
>>>
>>> rcoulomb = 1.2 ; short-range electrostatic cutoff
>>> (in
>>> nm)
>>>
>>> vdwtype = switch
>>> rvdw = 1.2 ; short-range van der Waals cutoff
>>> (in
>>> nm)
>>> rvdw_switch = 0.8
>>>
>>> pbc = xyz ; Direction in which to use Perodic Boundary
>>> Conditions (xyz, xy, no)
>>>
>>> ; Parameters for treating bonded interactions
>>> continuation = no ; Whether a fresh start or a continuation
>>> from
>>> a previous run (yes/no)
>>> constraint_algorithm = LINCS ; Constraint algorithm (LINCS / SHAKE)
>>> constraints = all-bonds ; Which bonds/angles to constrain
>>> (all-bonds
>>> / hbonds / none / all-angles / h-angles)
>>> 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)
>>>
>>> ; Parameters for treating electrostatic interactions
>>> coulombtype = PME ; Long range electrostatic interactions
>>> treatment (cut-off, Ewald, PME)
>>> pme_order = 4 ; Interpolation order for PME (cubic
>>> interpolation
>>> is represented by 4)
>>> fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using
>>> PME (nm)
>>>
>>> ; 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 = 300 300 ; 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)
>>>
>>> ; Miscellaneous control parameters
>>> ; Dispersion correction
>>> DispCorr = EnerPres ; Dispersion corrections for Energy and
>>> Pressure for vdW cut-off
>>> ; Initial Velocity Generation
>>> gen_vel = no ; Velocity is read from the previous run
>>> ; Centre of mass (COM) motion removal relative to the specified groups
>>> 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
>>> ------------------------------------------------------------
>>> -----------------------------------------------
>>> Any suggestions would be appreciated.
>>>
>>> Thanks,
>>> Tarak
>>>
>>>
>> --
>> ==================================================
>>
>> 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
>>
>> ==================================================
>> --
>> Gromacs Users mailing list
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