[gmx-users] Distance restrain with dummy atom

[Justin Lemkul]

On 8/11/15 11:06 AM, anu chandra wrote:
> Dear Justin,
>
> Thanks for your quick reply.
>
> I am trying to run membrane protein simulation with slab geometry and EW3DC
> method (ewald-geometry = 3dc), due to ion asymmetry in the system.
> Following the article
> http://www.cell.com/biophysj/abstract/S0006-3495%2803%2974458-0?mobileUi=0
> , I have set up my system with extended Z-dimension and used pbc = xyz.
> Unfortunately, when I carry out equilibration with EW3DC method and
> pbc=xyz, the membrane got distorted and become leaky. So, I trying to
> restraining water within a specific distance might help me to come out this
> problem. Below, I just copied the mdp file I am using for equilibration
> with slab geometry. If possible, please have a look and let me know
> valuable suggestion in this regard.
>

Use walls or a flat-bottom restraint and normal PBC/PME.

-Justin

> define                  = -DPOSRES_ON
> integrator              = md
> dt                      = 0.001
> nsteps                  = 25000
> nstlog                  = 1000
> nstxout                 = 1000
> nstvout                 = 1000
> nstfout                 = 1000
> nstcalcenergy           = 100
> nstenergy               = 1000
> ;
> cutoff-scheme           = Verlet
> nstlist                 = 20
> rlist                   = 1.2
> coulombtype             = pme
> rcoulomb                = 1.2
> vdwtype                 = Cut-off
> vdw-modifier            = Force-switch
> rvdw_switch             = 1.0
> rvdw                    = 1.2
> ;
> ewald-geometry          = 3dc              ;slab geometry
> pbc                     = xyz
> ;
> tcoupl                  = V-rescale
> tc_grps                 = Protein POPC Cal_CL_SOL
> tau_t                   = 0.5    0.5     0.5
> ref_t                   = 305.0    305.0    305.0
> ;
> pcoupl                  = Parrinello-Rahman
> pcoupltype              = semiisotropic
> tau_p                   = 5.0     5.0
> compressibility         = 4.5e-5  0   ;0 for z-direction due to vaccum slab
> ref_p                   = 1.0     1.0
> ;
> constraints             = h-bonds
> constraint_algorithm    = LINCS
> continuation            = yes
> ;
> nstcomm                 = 100
> comm_mode               = linear
> comm_grps               = Protein_POPC Cal_CL_SOL
> ;
> refcoord_scaling        = com
>
>
> Many thanks
> Anu
>
> On Tue, Aug 11, 2015 at 3:06 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 8/11/15 8:30 AM, anu chandra wrote:
>>
>>> Dear Gromacs users,
>>>
>>> I am working with membrane simulations and I would like to put distance
>>> restrain along Z-axis between a dummy atom I generated at the centre of
>>> box
>>> and all the water molecules. For this, I first generated a dummy atom at
>>> the centre of box and also made a simple .itp file for it as shown below,
>>>
>>> [ moleculetype ]
>>> ; molname   nrexcl
>>> DUM     1
>>>
>>> [ atoms ]
>>> ; id    at type     res nr  residu name at name  cg nr  charge
>>> 1   MW      1   DUM     DUM  0  0  1
>>>
>>>
>>> I am using charmm36 ff and atom type MW is special dummy particle mention
>>> in the charmm36 ffnonbonded.itp file, as shown below.
>>>
>>> ; special dummy-type particles
>>> MNH3    0   0.000000    0.00    A   0.0 0.0
>>> MNH2    0   0.000000    0.00    A   0.0 0.0
>>> MCH3    0   0.000000    0.00    A   0.0 0.0
>>> MCH3S   0   0.000000    0.00    A   0.0 0.0
>>> *MW *
>>> * 0   0.000000    0.00    A   0.0 0.0*
>>> Am I doing it correct here, for generating a dummy atom? Am I doing
>>> correct
>>> with provide hydrogen mass to dummy atom?
>>>
>>> Few other queries regarding the distance restrain are,
>>>
>>> 1. How do I make sure that the dummy atom do not fly away from the centre
>>> of box?
>>>
>>> 2. What steps I should take to generate a file for distance restrain
>>> between dummy atom and water molecules?
>>>
>>> Please help me to clarify these queries. Waiting for your valuable reply.
>>>
>>>
>> The better approach is to use the pull code, rather than layering on all
>> this complexity.  But perhaps the ultimate question is - why do you need to
>> restrain all the waters to be within some distance of the membrane?
>>
>> -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

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