[gmx-users] Distance restrain with dummy atom
Justin Lemkul
jalemkul at vt.edu
Wed Aug 12 22:38:57 CEST 2015
On 8/12/15 10:24 AM, anu chandra wrote:
> Dear Justin,
>
> Thanks for the reply. As you suggested I have tried with flat-bottomed
> position restraint. Unfortunately, the water molecules were seen to be
> moving to vacuum that leads to membrane distortion. The methodology I
> adopted is as follows,
>
> 1. I done 5 ns equilibration of protein-membrane-water system. Later, I
> added ions to upper water layer. The box dimension of equilibrated system
> is 112.347 112.347 126.531 90.00 90.00 90.00.
>
> 2. Then I added a ~12nm vacuum slab along z-axis above and below the
> membrane using editconf command -
>
> editconf -f input.gro -o ouput.gro -c -box
> 11.2347 11.2347 37.9593
>
With walls or a flat-bottom restraint, additional vacuum space is unnecessary.
Your distortion could be due to surface tension effects.
>
> 3. The 'output.gro' file from above step used for flat-bottomed position
> restraint simulation, where flat-bottomed position restraint applied on
> water and ions . The topology file looks as shown below,
>
> **************************************************************
> #include "POT.itp"
>
> #ifdef POSRES_ION
> ; Position restraint for potassium
> [ position_restraints ]
> ; i funct g r k
> 1 2 5 1 1000
> #endif
>
>
> #include "CL.itp"
>
> #ifdef POSRES_ION
> ; Position restraint for chloride
> [ position_restraints ]
> ; i funct g r k
> 1 2 5 1 1000
> #endif
>
> ; Include water topology
> #include "charmm36-jun2015.ff/tip3p.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for water
> [ position_restraints ]
> ; i funct g r k
> 1 2 5 1 1000
> 2 2 5 1 1000
> 3 2 5 1 1000
> #endif
> *************************************************************
>
> Here, I used layer geometry along z-axis and thickness of 1 nm. I have even
> tried with using thickness of half of the box length ( where the box length
> is excluded of vacuum slab) and also with restraining water oxygen alone.
> Unfortunately, all my trials has lead to water molecules flying to vacuum
> and membrane get distorted. Below is the mdp file is used for the
> simulation,
>
Presumably because you're allowing them to. What you're saying is "allow these
atoms to move freely within 1 nm of where they are right now." That's not what
you want. What you should do is construct a reference coordinate file (to be
passed to grompp -r) that has the z-coordinate of any restrained atom set to a
value of z/2 (easily done in a text editor). Then the restraint should be set
to z/2 as well, which means those restrained species are allowed to move freely
within half of the box. You should only have to apply the restraint to the
ions, not the waters (assuming you eliminate the presumably unnecessary vacuum
layer).
-Justin
> ******************************************************************
> define = -DPOSRES_ION -DPOSRES_WATER
> integrator = md
> dt = 0.001
> nsteps = 10000
> 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
> 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
> ;
> constraints = h-bonds
> constraint_algorithm = LINCS
> ;
> nstcomm = 100
> comm_mode = linear
> comm_grps = Protein_POPC Cal_CL_SOL
> ;
> gen-vel = yes
> gen-temp = 305.0
> gen-seed = -1
> ;
> refcoord_scaling = com
>
> ******************************************************************************************
>
> Can you please help me to figure out what is going wrong with the position
> restraint and simulation?
>
>
> Many thanks in advance
> Anu
>
>
> On Wed, Aug 12, 2015 at 12:44 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> 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
>>
>> ==================================================
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>> Gromacs Users mailing list
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>> * Please search the archive at
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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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