[gmx-users] au--protein separate equilibration
1. For separate equilibration of AU and Protein, I'm using this em.mdp file for equilibration in step 1, that Protein and SOL are frozen: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 nsteps = 4 ;constraint_algorithm = shake ;shake_tol = 0.0001 ;nstenergy = 10 ;nstxtcout = 10 ;nstlist = 5 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 freezegrps = Protein SOL freezedim = Y Y Y Y Y Y comm_mode = None 2. And in step 2 of equilibration (that AU is freezed), em2.mdp file contain: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 nsteps = 4 ;constraint_algorithm = shake ;shake_tol = 0.0001 ;nstenergy = 10 ;nstxtcout = 10 ;nstlist = 5 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 freezegrps = AU AUI AUC freezedim = Y Y Y Y Y Y Y Y Y comm_mode = None 3. In simulation, I'm using this md.mdp file: title = Yo cpp = /lib/cpp define = integrator = md tinit = 0.0 dt = 0.002 nsteps = 25 nstxout = 2500 nstvout = 2500 nstlog = 500 nstenergy = 250 nstxtcout = 0 pbc = xyz rlist = 1.00 coulombtype = PME r_coulomb = 1.00 fourierspacing = 0.10 pme_order = 6 ewald_rtol = 1e-6 vdw-type = switch rvdw-switch = 0.90 rvdw = 1.00 tcoupl = nose-hoover tc_grps = SOL AUS AUB AUI tau_t = 0.1 0.1 0.1 0.1 ref_t = 300 300 300 300 Pcoupl = no gen_vel = yes gen_temp = 10 gen_seed = 173529 ; GolP has been tested with lincs only constraints = none constraint_algorithm = lincs lincs_order = 4 lincs_iter = 1 lincs_warnangle = 80 freezegrps = AU AUI freezedim = Y Y Y Y Y Y comm_mode = None Are these .mdp file right? Fatemeh Ramezani -- 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
Re: [gmx-users] au--protein separate equilibration
On 1/17/13 12:15 PM, fatemeh ramezani wrote: 1. For separate equilibration of AU and Protein, I'm using this em.mdp file for equilibration in step 1, that Protein and SOL are frozen: This is not an equilibration, this is an energy minimization, which will likely not accomplish much with so many particles frozen. title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 nsteps = 4 ;constraint_algorithm = shake ;shake_tol = 0.0001 ;nstenergy = 10 ;nstxtcout = 10 ;nstlist = 5 ns_type = grid rlist = 1 coulombtype = PME rcoulomb= 1 rvdw= 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 freezegrps = Protein SOL freezedim = Y Y YY Y Y comm_mode = None I suppose this .mdp file will allow whatever the Au particle is to move, but I don't see much point to running anything where the solvent is frozen. Freezing water also makes -DFLEXBILE irrelevant. 2. And in step 2 of equilibration (that AU is freezed), em2.mdp file contain: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 nsteps = 4 ;constraint_algorithm = shake ;shake_tol = 0.0001 ;nstenergy = 10 ;nstxtcout = 10 ;nstlist = 5 ns_type = grid rlist = 1 coulombtype = PME rcoulomb= 1 rvdw= 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 freezegrps =AU AUI AUC freezedim = Y Y Y Y Y Y Y Y Y comm_mode = None 3. In simulation, I'm using this md.mdp file: title= Yo cpp = /lib/cpp define = integrator = md tinit= 0.0 dt = 0.002 nsteps = 25 nstxout = 2500 nstvout = 2500 nstlog = 500 nstenergy= 250 nstxtcout= 0 pbc = xyz rlist= 1.00 coulombtype = PME r_coulomb= 1.00 The correct keyword is rcoulomb. fourierspacing = 0.10 Why switch the fourierspacing here? You used 0.12 before, and now you'r eusing 0.10. pme_order= 6 ewald_rtol = 1e-6 vdw-type = switch rvdw-switch = 0.90 rvdw = 1.00 These vdw settings are all very different from the previous minimization step. It's usually a good idea to keep the settings the same throughout all steps, otherwise you're using some broken form of a force field intermittently. tcoupl = nose-hoover tc_grps = SOL AUS AUB AUI tau_t= 0.1 0.1 0.1 0.1 ref_t= 300 300 300 300 Depending on the size of these groups, assigning them to separate thermostats may not be appropriate, and it doesn't appear that the protein is coupled anywhere. Consult http://www.gromacs.org/Documentation/Terminology/Thermostats Pcoupl = no gen_vel = yes gen_temp = 10 gen_seed = 173529 ; GolP has been tested with lincs only Then why turn off constraints? constraints = none constraint_algorithm = lincs lincs_order = 4 lincs_iter = 1 lincs_warnangle = 80 freezegrps = AU AUI freezedim= Y Y Y Y Y Y comm_mode = None Are these .mdp file right? No. See points above. I can't comment on whether any of the settings are correct for use with the GolP force field, but there are numerous inconsistencies from a generic standpoint. -Justin -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at
Fw: [gmx-users] au--protein separate equilibration
Dear Justin thanks for your reply and, Please help me to correct the settings of .mdp files step by step . By these em.mdp files if I freeze only protein for the first time and after minimization I use the result .pdb file for second step of minimization that I freeze AU atoms in it, minimization would be true? title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 nsteps = 4 ;constraint_algorithm = shake ;shake_tol = 0.0001 ;nstenergy = 10 ;nstxtcout = 10 ;nstlist = 5 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 freezegrps = Protein freezedim = Y Y Y comm_mode = None 2. And in step 2 of equilibration (that AU is freezed), em2.mdp file contain: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints = none integrator = steep dt = 0.002 nsteps = 4 ;constraint_algorithm = shake ;shake_tol = 0.0001 ;nstenergy = 10 ;nstxtcout = 10 ;nstlist = 5 ns_type = grid rlist = 1 coulombtype = PME rcoulomb = 1 rvdw = 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 freezegrps = AU AUI AUC freezedim = Y Y Y Y Y Y Y Y Y comm_mode = None -- 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
Re: [gmx-users] au--protein separate equilibration
On 1/17/13 2:48 PM, fatemeh ramezani wrote: Dear Justin thanks for your reply and, Please help me to correct the settings of .mdp files step by step . I did that in my previous reply. By these em.mdp files if I freeze only protein for the first time and after minimization I use the result .pdb file for second step of minimization that I freeze AU atoms in it, minimization would be true? I don't understand the purpose of freezing anything during EM; that sort of defeats the purpose of optimizing geometry. You can approach your problem however you see fit. -Justin title = n.pdb cpp= /lib/cpp define = -DFLEXIBLE constraints= none integrator = steep dt = 0.002 nsteps = 4 ;constraint_algorithm = shake ;shake_tol = 0.0001 ;nstenergy = 10 ;nstxtcout = 10 ;nstlist= 5 ns_type= grid rlist = 1 coulombtype= PME rcoulomb= 1 rvdw= 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 freezegrps = Protein freezedim = Y Y Y comm_mode = None 2. And in step 2 of equilibration (that AU is freezed), em2.mdp file contain: title = n.pdb cpp = /lib/cpp define = -DFLEXIBLE constraints= none integrator = steep dt = 0.002 nsteps = 4 ;constraint_algorithm = shake ;shake_tol = 0.0001 ;nstenergy = 10 ;nstxtcout = 10 ;nstlist= 5 ns_type= grid rlist = 1 coulombtype= PME rcoulomb = 1 rvdw= 1.2 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft= yes ; Energy minimizing stuff emtol = 1000.0 emstep = 0.01 freezegrps =AU AUIAUC freezedim = Y Y Y Y Y Y Y Y Y comm_mode = None -- Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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
