Dear Justin, Thank you very much.
Sincerely, Mijiddorj > > ------------------------------ > > Message: 5 > Date: Sun, 4 Dec 2016 18:04:16 -0500 > From: Justin Lemkul <jalem...@vt.edu> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] COM group of Membrane and Protein simulation > Message-ID: <b811b475-566c-34f8-c16a-8aa43f7a9...@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 <jalem...@vt.edu> > >> To: gmx-us...@gromacs.org > >> Subject: Re: [gmx-users] COM group of Membrane and Protein simulation > >> Message-ID: <cc3fc878-feef-4424-dacd-3824d67a6...@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 > >> > >> jalem...@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 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > > > ------------------------------ > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? 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