Re: [gmx-users] Sudden increase in RMSD values for 100ns simulation of protein-protein complex
On 3/14/18 12:19 PM, SHYANTANI MAITI wrote: Dear all, I have been simulating a protein-protein complex using gromacs for 100ns. after the completion of job, I find that the rmsd values have undergone a sudden increase after 20ns of the simulation. Is my simulation going wrong somewhere? Can protein-protein complexes be simulated in gromacs? Did you try the suggestion I already provided? https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-March/119145.html -Justin -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Sudden increase in RMSD values for 100ns simulation of protein-protein complex
There are a number of papers where you can find RMSD plots for different protein-protein complex MD simulations. Please look into the literature to find out how others have done this. On Wed, Mar 14, 2018 at 5:19 PM, SHYANTANI MAITI wrote: > Dear all, > I have been simulating a protein-protein complex using gromacs for 100ns. > after the completion of job, I find that the rmsd values have undergone a > sudden increase after 20ns of the simulation. Is my simulation going wrong > somewhere? Can protein-protein complexes be simulated in gromacs? > > -- > Best regards, > *Shyantani Maiti* > -- > 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. > -- Joe Jordan -- 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] Sudden increase in RMSD values for 100ns simulation of protein-protein complex
Dear all, I have been simulating a protein-protein complex using gromacs for 100ns. after the completion of job, I find that the rmsd values have undergone a sudden increase after 20ns of the simulation. Is my simulation going wrong somewhere? Can protein-protein complexes be simulated in gromacs? -- Best regards, *Shyantani Maiti* -- 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] Sudden increase in RMSD values for 100ns simulation of protein-protein complex
On 3/12/18 3:26 PM, SHYANTANI MAITI wrote: Dear all, I have been simulating a protein-protein complex using gromacs for 100ns. after the completion of job, I find that the rmsd values have undergone a sudden increase after 20ns of the simulation. Is my simulation going wrong somewhere? Can protein-protein complexes be simulated in gromacs? Following is the final mdp file for simulating my protein-protein complex. Probably a PBC issue. Use trjconv to re-center everything before computing RMSD. -Justin title= MD simulation ; Run parameters integrator= md; leap-frog integrator nsteps= 5000; 2 * 5000 = 10 ps (100 ns) dt= 0.002; 2 fs ; Output control nstxout= 5000; save coordinates every 10.0 ps nstvout= 5000; save velocities every 10.0 ps nstenergy= 5000; save energies every 10.0 ps nstlog= 5000; update log file every 10.0 ps nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps ; nstxout-compressed replaces nstxtcout compressed-x-grps = System; replaces xtc-grps ; Bond parameters continuation= yes; Restarting after NPT constraint_algorithm= lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type= grid; search neighboring grid cells nstlist= 10; 20 fs, largely irrelevant with Verlet scheme rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.1 0.1; time constant, in ps ref_t= 300 300; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Berendsen; Pressure coupling on in NPT pcoupltype= isotropic; uniform scaling of box vectors tau_p= 2.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= no; Velocity generation is off -- == Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html == -- 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] Sudden increase in RMSD values for 100ns simulation of protein-protein complex
Dear all, I have been simulating a protein-protein complex using gromacs for 100ns. after the completion of job, I find that the rmsd values have undergone a sudden increase after 20ns of the simulation. Is my simulation going wrong somewhere? Can protein-protein complexes be simulated in gromacs? Following is the final mdp file for simulating my protein-protein complex. title= MD simulation ; Run parameters integrator= md; leap-frog integrator nsteps= 5000; 2 * 5000 = 10 ps (100 ns) dt= 0.002; 2 fs ; Output control nstxout= 5000; save coordinates every 10.0 ps nstvout= 5000; save velocities every 10.0 ps nstenergy= 5000; save energies every 10.0 ps nstlog= 5000; update log file every 10.0 ps nstxout-compressed = 5000 ; save compressed coordinates every 10.0 ps ; nstxout-compressed replaces nstxtcout compressed-x-grps = System; replaces xtc-grps ; Bond parameters continuation= yes; Restarting after NPT constraint_algorithm= lincs; holonomic constraints constraints= all-bonds; all bonds (even heavy atom-H bonds) constrained lincs_iter= 1; accuracy of LINCS lincs_order= 4; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type= grid; search neighboring grid cells nstlist= 10; 20 fs, largely irrelevant with Verlet scheme rcoulomb= 1.0; short-range electrostatic cutoff (in nm) rvdw= 1.0; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald for long-range electrostatics pme_order= 4; cubic interpolation fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on tcoupl= V-rescale; modified Berendsen thermostat tc-grps= Protein Non-Protein; two coupling groups - more accurate tau_t= 0.1 0.1; time constant, in ps ref_t= 300 300; reference temperature, one for each group, in K ; Pressure coupling is on pcoupl= Berendsen; Pressure coupling on in NPT pcoupltype= isotropic; uniform scaling of box vectors tau_p= 2.0; time constant, in ps ref_p= 1.0; reference pressure, in bar compressibility = 4.5e-5; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc= xyz; 3-D PBC ; Dispersion correction DispCorr= EnerPres; account for cut-off vdW scheme ; Velocity generation gen_vel= no; Velocity generation is off -- Best regards, *Shyantani Maiti* -- 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.
