Aw: Re: [gmx-users] Constant-Force Pulling of Ubiquitin
I dont know how well v-rescale works with pulling. It could be after removing some restraints it still had not reached a good equilibrium (ie let it run a while/nanosecound or 5, before pulling it), or maybe generating velocities on start causes more caos than the proteins or system can handle, still it may be the real system minus several initial time frames, ie it either isnt bound from the start as it is in reality or it prefers to be free...But I may be wrong on some of this...so just suggestions. Also, 500 picoseconds is short for measring things, and would probably be dominated by starting velocity for at least 40-80 picoseconds, thus look at how fast it declines...there are some printed standards for protein-protein delG or domain changes of around 3-4 ns to make sure small loop/domain changes are represented in the energy profile. There was (on some comments) talk of making this around 6 ns..but I dont know if there are set real standards for this held fast to (i've read 2 papers with 400 ns to see domain changes with no pull, and a good 5-6 at 4 ns with pulling so?). Stephan Wakins Gesendet: Dienstag, 29. Oktober 2013 um 20:27 Uhr Von: "XAvier Periole" An: "Discussion list for GROMACS users" Betreff: Re: [gmx-users] Constant-Force Pulling of Ubiquitin You want to switch to sd instead of md. > On Oct 29, 2013, at 17:43, Vivian wrote: > > Hi GMX Users, > > I am using Gromacs (Version 4.5.5) to do constant-force pulling of ubiquitin > and it's a implicit model. My mdp file for pulling is shown as following. > > integrator = md > dt = 0.001 ; ps ! > nsteps = 50 ; total 500 ps. > > nstxout = 100 > nstvout = 100 > nstfout = 100 > nstlist = 10 > nstlog = 100 > nstcalcenergy =100 > > rlist = 5 > rvdw = 5 > rcoulomb = 5 > coulombtype = cut-off > vdwtype = cut-off > table-extension = 5 > bd_fric = 0 > ld_seed = -1 > pbc = no > ns_type = simple > constraints = all-bonds > lincs_order = 4 > lincs_iter = 1 > lincs-warnangle = 30 > > Tcoupl = v-rescale > tau_t = 1.0 > tc-grps = Protein > ref_t = 300 > > Pcoupl = no > > gen_vel = yes > gen_temp = 300 > gen_seed = 173529 > > comm_mode = Angular > nstcomm =100 > > > ; IMPLICIT SOLVENT ALGORITHM > implicit_solvent = gbsa > > ; GENERALIZED BORN ELECTROSTATICS > ; Algorithm for calculating Born radii > gb_algorithm = Still > ; Frequency of calculating the Born radii inside rlist > nstgbradii = 1 > ; Cutoff for Born radii calculation; the contribution from atoms > ; between rlist and rgbradii is updated every nstlist steps > rgbradii = 5 > ; Dielectric coefficient of the implicit solvent > gb_epsilon_solvent = 80 > ; Salt concentration in M for Generalized Born models > gb_saltconc = 0 > ; Scaling factors used in the OBC GB model. Default values are OBC(II) > gb_obc_alpha = 1 > gb_obc_beta = 0.8 > gb_obc_gamma = 4.85 > gb_dielectric_offset = 0.009 > sa_algorithm = Ace-approximation > ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA > ; The value -1 will set default value for Still/HCT/OBC GB-models. > sa_surface_tension = 2.05016 > > ; Pull code > pull = constant_force > ;Center of mass pulling using a linear potential and therefore a constant > force. > pull_geometry = direction > pull_start = yes ; define initial COM distance > 0 > pull_ngroups = 1 > pull_group1 = Chain_B > pull_group0 = Chain_A > pull_k1 = -500 ; kJ mol^-1 nm^-2 > pull_vec1 = 0.0 0.0 1.0 > > However, after pulling simulation, it turns out the potential of this system > becomes lower rather than higher (from -1 to -2). It's very wired > since potential should become larger after pulling. > Here is the notification after g_energy: > > Energy Average Err.Est. RMSD Tot-Drift > --- > Potential -20734.5 230 1268.47 -1385.71 > (kJ/mol) > > You may want to use the -driftcorr flag in order to correct for spurious > drift in the graphs. Note that this is not > a substitute for proper equilibration and sampling! You should select the > temperature in order to obtain fluctuation properties. > > I wonder whether there is any problem with my mdp file. > Thank you so much!! > > Best, > Vivian > > -- > View this message in context: http://gromacs.5086.x6.nabble.com/Constant-Force-Pulling-of-Ubiquitin-tp5012065.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don'
Re: [gmx-users] Constant-Force Pulling of Ubiquitin
You want to switch to sd instead of md. > On Oct 29, 2013, at 17:43, Vivian wrote: > > Hi GMX Users, > > I am using Gromacs (Version 4.5.5) to do constant-force pulling of ubiquitin > and it's a implicit model. My mdp file for pulling is shown as following. > > integrator = md > dt = 0.001; ps ! > nsteps = 50 ; total 500 ps. > > nstxout = 100 > nstvout = 100 > nstfout = 100 > nstlist = 10 > nstlog = 100 > nstcalcenergy=100 > > rlist = 5 > rvdw = 5 > rcoulomb = 5 > coulombtype = cut-off > vdwtype = cut-off > table-extension = 5 > bd_fric = 0 > ld_seed = -1 > pbc = no > ns_type = simple > constraints = all-bonds > lincs_order = 4 > lincs_iter = 1 > lincs-warnangle = 30 > > Tcoupl = v-rescale > tau_t = 1.0 > tc-grps = Protein > ref_t = 300 > > Pcoupl = no > > gen_vel = yes > gen_temp= 300 > gen_seed= 173529 > > comm_mode = Angular > nstcomm =100 > > > ; IMPLICIT SOLVENT ALGORITHM > implicit_solvent = gbsa > > ; GENERALIZED BORN ELECTROSTATICS > ; Algorithm for calculating Born radii > gb_algorithm = Still > ; Frequency of calculating the Born radii inside rlist > nstgbradii = 1 > ; Cutoff for Born radii calculation; the contribution from atoms > ; between rlist and rgbradii is updated every nstlist steps > rgbradii = 5 > ; Dielectric coefficient of the implicit solvent > gb_epsilon_solvent = 80 > ; Salt concentration in M for Generalized Born models > gb_saltconc = 0 > ; Scaling factors used in the OBC GB model. Default values are OBC(II) > gb_obc_alpha = 1 > gb_obc_beta = 0.8 > gb_obc_gamma = 4.85 > gb_dielectric_offset = 0.009 > sa_algorithm = Ace-approximation > ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA > ; The value -1 will set default value for Still/HCT/OBC GB-models. > sa_surface_tension = 2.05016 > > ; Pull code > pull= constant_force > ;Center of mass pulling using a linear potential and therefore a constant > force. > pull_geometry = direction > pull_start = yes ; define initial COM distance > 0 > pull_ngroups= 1 > pull_group1 = Chain_B > pull_group0 = Chain_A > pull_k1 = -500 ; kJ mol^-1 nm^-2 > pull_vec1 = 0.0 0.0 1.0 > > However, after pulling simulation, it turns out the potential of this system > becomes lower rather than higher (from -1 to -2). It's very wired > since potential should become larger after pulling. > Here is the notification after g_energy: > > Energy Average Err.Est. RMSD Tot-Drift > --- > > Potential -20734.52301268.47 -1385.71 > (kJ/mol) > > You may want to use the -driftcorr flag in order to correct for spurious > drift in the graphs. Note that this is not > a substitute for proper equilibration and sampling! You should select the > temperature in order to obtain fluctuation properties. > > I wonder whether there is any problem with my mdp file. > Thank you so much!! > > Best, > Vivian > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/Constant-Force-Pulling-of-Ubiquitin-tp5012065.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Constant-Force Pulling of Ubiquitin
Hi GMX Users, I am using Gromacs (Version 4.5.5) to do constant-force pulling of ubiquitin and it's a implicit model. My mdp file for pulling is shown as following. integrator = md dt = 0.001; ps ! nsteps = 50 ; total 500 ps. nstxout = 100 nstvout = 100 nstfout = 100 nstlist = 10 nstlog = 100 nstcalcenergy =100 rlist = 5 rvdw = 5 rcoulomb = 5 coulombtype = cut-off vdwtype = cut-off table-extension = 5 bd_fric = 0 ld_seed = -1 pbc = no ns_type = simple constraints = all-bonds lincs_order = 4 lincs_iter = 1 lincs-warnangle = 30 Tcoupl = v-rescale tau_t = 1.0 tc-grps = Protein ref_t = 300 Pcoupl = no gen_vel = yes gen_temp= 300 gen_seed= 173529 comm_mode = Angular nstcomm =100 ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = gbsa ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 5 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The value -1 will set default value for Still/HCT/OBC GB-models. sa_surface_tension = 2.05016 ; Pull code pull= constant_force ;Center of mass pulling using a linear potential and therefore a constant force. pull_geometry = direction pull_start = yes ; define initial COM distance > 0 pull_ngroups= 1 pull_group1 = Chain_B pull_group0 = Chain_A pull_k1 = -500 ; kJ mol^-1 nm^-2 pull_vec1 = 0.0 0.0 1.0 However, after pulling simulation, it turns out the potential of this system becomes lower rather than higher (from -1 to -2). It's very wired since potential should become larger after pulling. Here is the notification after g_energy: Energy Average Err.Est. RMSD Tot-Drift --- Potential -20734.52301268.47 -1385.71 (kJ/mol) You may want to use the -driftcorr flag in order to correct for spurious drift in the graphs. Note that this is not a substitute for proper equilibration and sampling! You should select the temperature in order to obtain fluctuation properties. I wonder whether there is any problem with my mdp file. Thank you so much!! Best, Vivian -- View this message in context: http://gromacs.5086.x6.nabble.com/Constant-Force-Pulling-of-Ubiquitin-tp5012065.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Constant-Force Pulling of Ubiquitin
Hi GMX Users, I am using Gromacs (Version 4.5.5) to do constant-force pulling of ubiquitin and it's a implicit model. My mdp file for pulling is shown as following. integrator = md dt = 0.001; ps ! nsteps = 50 ; total 500 ps. nstxout = 100 nstvout = 100 nstfout = 100 nstlist = 10 nstlog = 100 nstcalcenergy =100 rlist = 5 rvdw = 5 rcoulomb = 5 coulombtype = cut-off vdwtype = cut-off table-extension = 5 bd_fric = 0 ld_seed = -1 pbc = no ns_type = simple constraints = all-bonds lincs_order = 4 lincs_iter = 1 lincs-warnangle = 30 Tcoupl = v-rescale tau_t = 1.0 tc-grps = Protein ref_t = 300 Pcoupl = no gen_vel = yes gen_temp= 300 gen_seed= 173529 comm_mode = Angular nstcomm =100 ; IMPLICIT SOLVENT ALGORITHM implicit_solvent = gbsa ; GENERALIZED BORN ELECTROSTATICS ; Algorithm for calculating Born radii gb_algorithm = Still ; Frequency of calculating the Born radii inside rlist nstgbradii = 1 ; Cutoff for Born radii calculation; the contribution from atoms ; between rlist and rgbradii is updated every nstlist steps rgbradii = 5 ; Dielectric coefficient of the implicit solvent gb_epsilon_solvent = 80 ; Salt concentration in M for Generalized Born models gb_saltconc = 0 ; Scaling factors used in the OBC GB model. Default values are OBC(II) gb_obc_alpha = 1 gb_obc_beta = 0.8 gb_obc_gamma = 4.85 gb_dielectric_offset = 0.009 sa_algorithm = Ace-approximation ; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA ; The value -1 will set default value for Still/HCT/OBC GB-models. sa_surface_tension = 2.05016 ; Pull code pull= constant_force ;Center of mass pulling using a linear potential and therefore a constant force. pull_geometry = direction pull_start = yes ; define initial COM distance > 0 pull_ngroups= 1 pull_group1 = Chain_B pull_group0 = Chain_A pull_k1 = -500 ; kJ mol^-1 nm^-2 pull_vec1 = 0.0 0.0 1.0 However, after pulling simulation, it turns out the potential of this system becomes lower rather than higher (from -1 to -2). It's very wired since potential should become larger after pulling. Here is the notification after g_energy: Energy Average Err.Est. RMSD Tot-Drift --- Potential -20734.52301268.47 -1385.71 (kJ/mol) You may want to use the -driftcorr flag in order to correct for spurious drift in the graphs. Note that this is not a substitute for proper equilibration and sampling! You should select the temperature in order to obtain fluctuation properties. I wonder whether there is any problem with my mdp file. Thank you so much!! Best, Vivian -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
