Re: [gmx-users] system cooling down when runing NVE
In general, NVE is tricky business, since small integration errors build up and cause energy drift in the long run. Do you see energy drift too? In my experience one needs double precision and a shorter timestep than what you employ. But that is of course system dependent. Erik 9 maj 2012 kl. 03.17 skrev Peter C. Lai: you have position restraints on, which I expect would damp collisions between solvent and solute. temp drops towards some sort of equilibrium, which doesn't necessarily match your starting temp even though energy of the system is conserved ..sounds like expected behavior to me? -- Sent from my Android phone with K-9 Mail. Please excuse my brevity. Thanh Binh NGUYEN nguye...@bii.a-star.edu.sg wrote: Dear Gromacs experts, I'm just a newbaby in Gromacs, and hence I have a lot of problem when running this program. I try to run NVE simulation of a protein. First, I run an NTP ensemble, follow by NVT and finally, NVE. In NPT and NVT, T remains as constant, however, in NVE simulation, the temperature drops gradually instead of maintain approximately constant. Could you give me any advice to solve this problem? Thank you very much. Regards, Nguyen P.S: below is my mdp file for three simulations: NPT ensemble: title = DEN2pro_MD define = -DFLEXIBLE constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 100 ; total 2000 ps. nstcomm = 1 nstxout = 5000 ; output coordinates every 10 ps nstvout = 5000 ; output velocities every 10 ps nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.1 0.1 tc_grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 br / NVT ensemble title = DEN2pro_MD NVT equilibration define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md; leap-frog integrator nsteps = 10 ; 2 * 10 = 200 ps dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 10 ps nstvout = 5000 ; save velocities every 10 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps energygrps = Protein ; Bond parameters continuation= no; first dynamics run constraint_algorithm = lincs; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS gt; lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; 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 off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed NVE ensemble: title = DEN2pro_MD NVE equilibration define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md-vv ; leap-frog integrator nsteps = 100 ; 2 * 100 = 2000 ps dt = 0.002 ; 2 fs ; Out put control nstxout = 5000 ; save coordinates every 10 ps nstvout = 5000 ; save velocities every 10 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps energygrps
[gmx-users] system cooling down when runing NVE
Dear Gromacs experts, I'm just a newbaby in Gromacs, and hence I have a lot of problem when running this program. I try to run NVE simulation of a protein. First, I run an NTP ensemble, follow by NVT and finally, NVE. In NPT and NVT, T remains as constant, however, in NVE simulation, the temperature drops gradually instead of maintain approximately constant. Could you give me any advice to solve this problem? Thank you very much. Regards, Nguyen P.S: below is my mdp file for three simulations: NPT ensemble: title = DEN2pro_MD define = -DFLEXIBLE constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 100 ; total 2000 ps. nstcomm = 1 nstxout = 5000 ; output coordinates every 10 ps nstvout = 5000 ; output velocities every 10 ps nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.1 0.1 tc_grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 NVT ensemble title = DEN2pro_MD NVT equilibration define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md; leap-frog integrator nsteps = 10 ; 2 * 10 = 200 ps dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 10 ps nstvout = 5000 ; save velocities every 10 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps energygrps = Protein ; Bond parameters continuation= no; first dynamics run 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 ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rvdw= 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; 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 off pcoupl = no; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr= EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp= 300 ; temperature for Maxwell distribution gen_seed= -1; generate a random seed NVE ensemble: title = DEN2pro_MD NVE equilibration define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md-vv ; leap-frog integrator nsteps = 100 ; 2 * 100 = 2000 ps dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 10 ps nstvout = 5000 ; save velocities every 10 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps energygrps = Protein ; Bond parameters continuation= no; first dynamics run 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 ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.6 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) rlistlong = 1.6 ;treatment of van der waals interactions vdwtype = Shift rvdw= 0.95 ; short-range van der Waals cutoff (in nm) rvdw-switch = 0.9 ; Electrostatics coulombtype = PME-Switch; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT ; Temperature coupling is on tcoupl = no
Re: [gmx-users] system cooling down when runing NVE
you have position restraints on, which I expect would damp collisions between solvent and solute. temp drops towards some sort of equilibrium, which doesn't necessarily match your starting temp even though energy of the system is conserved ..sounds like expected behavior to me? -- Sent from my Android phone with K-9 Mail. Please excuse my brevity. Thanh Binh NGUYEN nguye...@bii.a-star.edu.sg wrote: Dear Gromacs experts, I'm just a newbaby in Gromacs, and hence I have a lot of problem when running this program. I try to run NVE simulation of a protein. First, I run an NTP ensemble, follow by NVT and finally, NVE. In NPT and NVT, T remains as constant, however, in NVE simulation, the temperature drops gradually instead of maintain approximately constant. Could you give me any advice to solve this problem? Thank you very much. Regards, Nguyen P.S: below is my mdp file for three simulations: NPT ensemble: title = DEN2pro_MD define = -DFLEXIBLE constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 100 ; total 2000 ps. nstcomm = 1 nstxout = 5000 ; output coordinates every 10 ps nstvout = 5000 ; output velocities every 10 ps nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 0.9 coulombtype = PME rcoulomb = 0.9 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in four groups Tcoupl = berendsen tau_t = 0.1 0.1 tc_grps = protein non-protein ref_t = 300 300 ; Pressure coupling is on Pcoupl = berendsen pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 NVT ensemble title = DEN2pro_MD NVT equilibration define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md ; leap-frog integrator nsteps = 10 ; 2 * 10 = 200 ps dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 10 ps nstvout = 5000 ; save velocities every 10 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps energygrps = Protein ; Bond parameters continuation = no ; first dynamics run 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 ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 0.9 ; short-range neighborlist cutoff (in nm) rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm) rvdw = 1.4 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; 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 off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed NVE ensemble: title = DEN2pro_MD NVE equilibration define = -DPOSRES ; position restrain the protein and ligand ; Run parameters integrator = md-vv ; leap-frog integrator nsteps = 100 ; 2 * 100 = 2000 ps dt = 0.002 ; 2 fs ; Output control nstxout = 5000 ; save coordinates every 10 ps nstvout = 5000 ; save velocities every 10 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps energygrps = Protein ; Bond parameters continuation = no ; first dynamics run 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 ns_type = grid ; search neighboring grid cells nstlist = 5 ; 10 fs rlist = 1.6 ; short-range neighborlist cutoff (in nm) rcoulomb = 0.9 ; short-range electrostatic cutoff (in nm) rlistlong = 1.6 ;treatment of van der waals interactions vdwtype = Shift rvdw = 0.95 ; short-range van der Waals cutoff (in nm) rvdw-switch = 0.9 ; Electrostatics coulombtype = PME-Switch; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.12 ; grid spacing for FFT ; Temperature coupling is on tcoupl = no; no temperature coupling in NVE ; Pressure coupling is off pcoupl = no
