[gmx-users] Semiisotropic pressure coupling

Justin Lemkul jalemkul at vt.edu
Tue Feb 17 14:03:57 CET 2015



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

==================================================


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