[gmx-users] Semiisotropic pressure coupling
tarak karmakar
tarak20489 at gmail.com
Wed Feb 18 05:06:44 CET 2015
Oh! I see. Thanks for the information.
regards,
Tarak
On Tue, Feb 17, 2015 at 6:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 2/17/15 1:23 AM, tarak karmakar wrote:
>
>> 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.
>>
>>
> 3-4 ns is nothing for a membrane system. We have confirmed the APL is
> consistent in GROMACS, CHARMM, and NAMD over the course of 250-ns
> simulations, after throwing out the first 50 ns as equilibration. That
> time scale is typical for membrane systems.
>
> -Justin
>
>
> ------------------------------------------------------------
>> ----------------------------------------------------------------------
>> 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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> --
> ==================================================
>
> 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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--
*Tarak KarmakarMolecular Simulation Lab.Chemistry and Physics of Materials
UnitJawaharlal Nehru Centre for Advanced Scientific Research Jakkur P. O.
Bangalore - 560 064Karnataka, INDIAPh. (lab) : +91-80-22082809 *
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