[gmx-users] Distance restrain with dummy atom

[anu chandra]

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.

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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