[gmx-users] COM group of Membrane and Protein simulation

[Justin Lemkul]

On 12/2/16 10:29 PM, Mijiddorj Batsaikhan wrote:
> Dear Justin,
>
> Thank you very much.
> I attached my mdp file. Peptide locates on membrane surface. I want to know
> about interaction between membrane and peptide, membrane permeability of
> peptide, amino acids contribution for the penetration, specially energetic
> values between the membrane and the peptide.
> Please suggest me with helpful options?
> How can I chose COM groups?
>

This topic was recently discussed at great length on the list, and I believe the 
conclusion was that there was no really solid answer.  In biphasic systems, in 
which the two phases have different diffusion properties, typically the two 
phases are the two groups.  For a protein bound to a membrane, the protein is 
part of both environments.  I don't think it should be its own separate group, 
but there is no systematic study of simulation properties in this regard that I 
know of.

-Justin

> I also copied my mdp file.
>
> ================
> integrator              = md
> dt                      = 0.002
> nsteps                  = 25000000
> nstlog                  = 5000
> nstxout                 = 5000
> nstvout                 = 5000
> nstfout                 = 5000
> nstcalcenergy           = 100
> nstenergy               = 100
> nstxout-compressed      = 100
> nstxtcout               = 100
> compressed-x-grps       = System
> energygrps              = PROT MEMB SOL
> ;
> cutoff-scheme           = Verlet
> nstlist                 = 10
> rlist                   = 1.2
> coulombtype             = pme
> rcoulomb                = 1.2
> vdwtype                 = Cut-off
> vdw-modifier            = Force-switch
> rvdw_switch             = 1.0
> rvdw                    = 1.2
> ;
> tcoupl                  = Nose-Hoover
> tc_grps                 = PROT   MEMB   SOL_ION
> tau_t                   = 1.0    1.0    1.0
> ref_t                   = 313 313 313
> ;
> pcoupl                  = Parrinello-Rahman
> pcoupltype              = semiisotropic
> tau_p                   = 5.0
> compressibility         = 4.5e-5  4.5e-5
> ref_p                   = 1.0     1.0
> ;
> constraints             = h-bonds
> constraint_algorithm    = LINCS
> continuation            = yes
> ;
> nstcomm                 = 100
> comm_mode               = linear
> comm_grps               = PROT   MEMB   SOL_ION ; which one is better to
> the simulation?
> ;comm_grps               = PROT_MEMB   SOL_ION ; which one is better to the
> simulation?
> ;
> refcoord_scaling        = com
> ================
> ------------------------------
>
>>
>> Message: 5
>> Date: Fri, 2 Dec 2016 07:50:52 -0500
>> From: Justin Lemkul <jalemkul at vt.edu>
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] COM group of Membrane and Protein simulation
>> Message-ID: <cc3fc878-feef-4424-dacd-3824d67a6270 at vt.edu>
>> Content-Type: text/plain; charset=windows-1252; format=flowed
>>
>>
>>
>> On 12/1/16 9:17 PM, Mijiddorj Batsaikhan wrote:
>>> Dear gmx_users,
>>>
>>> I started simulation that a peptide on membrane. My peptide locates on
>> the
>>> membrane surface. I have two questions relating to the simulation.
>>> (1)
>>> When I start the simulation, I chose COM groups separately. Is this
>> choice
>>> okay? or May I need to chose COM group inseparately?
>>>
>>
>> Your description is ambiguous; please post the actual .mdp contents.
>>
>>> (2)
>>> During the simulation peptide is moving the edge of membrane. How can I
>>> shift the peptide to the central section of the membrane? Can I use
>>> -nojump, -center options of trjconv tool?
>>>
>>
>> Yes - try it and see.  Also relevant is -fit transxy.
>>
>> -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
>>
>> ==================================================
>>
>>
>>
>>

-- 
==================================================

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

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