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

[Mijiddorj Batsaikhan]

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?

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
>
> ==================================================
>
>