Re: [gmx-users] COM group of Membrane and Protein simulation
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 = 2500 > > 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 = 1.01.01.0 > > 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
Re: [gmx-users] COM group of Membrane and Protein simulation
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 = 2500 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 = 1.01.01.0 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? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] COM group of Membrane and Protein simulation
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 = 2500 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 = 1.01.01.0 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 > > == > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] COM group of Membrane and Protein simulation
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? -- > > 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 > > == > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] COM group of Membrane and Protein simulation
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 == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] COM group of Membrane and Protein simulation
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? (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? Best regards, Mijiddorj -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
