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

[Mijiddorj Batsaikhan]

Dear Justin,

Thank you very much.

Sincerely,

Mijiddorj


>
> ------------------------------
>
> Message: 5
> Date: Sun, 4 Dec 2016 18:04:16 -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: <b811b475-566c-34f8-c16a-8aa43f7a9f96 at vt.edu>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
>
>
> 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
>
> ==================================================
>
>
> ------------------------------
>
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> End of gromacs.org_gmx-users Digest, Vol 152, Issue 18
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