Re: [gmx-users] LINCS WARNING - Protein-Membrane-system
On 1/1/13 8:56 AM, Shima Arasteh wrote: Hi, I have a system of Peptide-popc-ions-water to simulate. I'm trying to run MD simulation following the Justin's tutorial of kalp15-DPPC. The force field which I use, is charmm36. In NVT step, I get LINCS-warning as follow: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 2.460224, max 54.696251 (between atoms 4719 and 4716) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.182707, max 15.613569 (between atoms 4725 and 4726) When I checked the warning, I see the first warning is related to 2 atoms of 71POPC, the chain of 71POPC residue is broken near these two atoms. And the other warning is related to a bond between H and C in the other POPC residue. Some settings of nvt.mdp is as: ns_type= grid nstlist= 5 rlist= 1.2 rlistlong = 1.4 rcoulomb= 1.2 rvdw= 1.2 pbc= xyz vdwtype = switch rvdw_switch = 0.8 ; Parameters for treating bonded interactions continuation= no constraint_algorithm = LINCS constraints= all-bonds lincs_iter= 1 lincs_order= 4 Do I need to increase the rlistlong? I have done a simulation of POPC-water before with these settings, but everything was ok. So what's the problem? Anybody may help me? Don't haphazardly mess with cutoffs. Doing so usually makes your problem worse. Think about it scientifically - if POPC/water worked fine, but a POPC/protein/water system doesn't, what's the variable that changed? Moreover, look at when the failure is happening - it's failing at step zero. LINCS warnings always have the same causes: 1. Wrong .mdp settings (likely not the case, see above) 2. Insufficient equilibration (well, yours is failing outright, so probably not) 3. Insufficient minimization (hmmm...) -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 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] LINCS WARNING - Protein-Membrane-system
Thanks. I compared settings of mdp files in POPC/WATER and POPC/PROTEIN/WATER systems. The only difference I found between them was about the bonds constraints. The constraints of mdp file for POPC/WATER was constraints = h-bonds , however it was constraints = all-bonds for POPC/PROTEIN/WATER system. You say insufficient minimization, I don't think so . I got a sensible potential energy as follow: Potential Energy = -1.2414742e+06 Maximum force = 9.8055229e+01 on atom 4719 Norm of force = 3.4904923e+00 Then what's wrong with the EM? Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, January 1, 2013 6:45 PM Subject: Re: [gmx-users] LINCS WARNING - Protein-Membrane-system On 1/1/13 8:56 AM, Shima Arasteh wrote: Hi, I have a system of Peptide-popc-ions-water to simulate. I'm trying to run MD simulation following the Justin's tutorial of kalp15-DPPC. The force field which I use, is charmm36. In NVT step, I get LINCS-warning as follow: Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 2.460224, max 54.696251 (between atoms 4719 and 4716) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length Step 0, time 0 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.182707, max 15.613569 (between atoms 4725 and 4726) When I checked the warning, I see the first warning is related to 2 atoms of 71POPC, the chain of 71POPC residue is broken near these two atoms. And the other warning is related to a bond between H and C in the other POPC residue. Some settings of nvt.mdp is as: ns_type = grid nstlist = 5 rlist = 1.2 rlistlong = 1.4 rcoulomb = 1.2 rvdw = 1.2 pbc = xyz vdwtype = switch rvdw_switch = 0.8 ; Parameters for treating bonded interactions continuation = no constraint_algorithm = LINCS constraints = all-bonds lincs_iter = 1 lincs_order = 4 Do I need to increase the rlistlong? I have done a simulation of POPC-water before with these settings, but everything was ok. So what's the problem? Anybody may help me? Don't haphazardly mess with cutoffs. Doing so usually makes your problem worse. Think about it scientifically - if POPC/water worked fine, but a POPC/protein/water system doesn't, what's the variable that changed? Moreover, look at when the failure is happening - it's failing at step zero. LINCS warnings always have the same causes: 1. Wrong .mdp settings (likely not the case, see above) 2. Insufficient equilibration (well, yours is failing outright, so probably not) 3. Insufficient minimization (hmmm...) -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 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] LINCS WARNING - Protein-Membrane-system
On 1/1/13 10:41 AM, Shima Arasteh wrote: Thanks. I compared settings of mdp files in POPC/WATER and POPC/PROTEIN/WATER systems. The only difference I found between them was about the bonds constraints. The constraints of mdp file for POPC/WATER was constraints = h-bonds , however it was constraints = all-bonds for POPC/PROTEIN/WATER system. You say insufficient minimization, I don't think so . I got a sensible potential energy as follow: Potential Energy = -1.2414742e+06 Maximum force = 9.8055229e+01 on atom 4719 Norm of force = 3.4904923e+00 Then what's wrong with the EM? Please post a complete .mdp file for both the EM and NVT processes. Without that information, it's pure guesswork. -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 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] LINCS WARNING - Protein-Membrane-system
Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, January 1, 2013 7:17 PM Subject: Re: [gmx-users] LINCS WARNING - Protein-Membrane-system On 1/1/13 10:41 AM, Shima Arasteh wrote: Thanks. I compared settings of mdp files in POPC/WATER and POPC/PROTEIN/WATER systems. The only difference I found between them was about the bonds constraints. The constraints of mdp file for POPC/WATER was constraints = h-bonds , however it was constraints = all-bonds for POPC/PROTEIN/WATER system. You say insufficient minimization, I don't think so . I got a sensible potential energy as follow: Potential Energy = -1.2414742e+06 Maximum force = 9.8055229e+01 on atom 4719 Norm of force = 3.4904923e+00 Then what's wrong with the EM? Please post a complete .mdp file for both the EM and NVT processes. Without that information, it's pure guesswork. -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 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'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
Re: [gmx-users] LINCS WARNING - Protein-Membrane-system
On 1/1/13 10:53 AM, Shima Arasteh wrote: If I tell you that I changed the constraints and now the NVT is running, would that be ok? However I don't know the scientific reason of this incident! But I bring you the EM.mdp as follow: define = -DSTRONG_POSRES integrator= steep; Algorithm (steep = steepest descent minimization) emtol= 100.0 ; Stop minimization when the maximum force 100.0 kJ/mol/nm emstep= 0.01 ; Energy step size nsteps= 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist= 1; Frequency to update the neighbor list and long range forces ns_type= grid; Method to determine neighbor list (simple, grid) rlist= 1.2; Cut-off for making neighbor list (short range forces) coulombtype= PME; Treatment of long range electrostatic interactions rcoulomb= 1.2; Short-range electrostatic cut-off rvdw= 1.2; Short-range Van der Waals cut-off pbc= xyz ; Periodic Boundary Conditions And the NVT.mdp as follow (after change of all-bond constraint to h-bond): title= NVT equilibration for dimer-POPC - CHARMM36 define= -DPOSRES; Protein is position restrained (uses the posres.itp file information) ; Parameters describing the details of the NVT simulation protocol integrator= md; Algorithm (md = molecular dynamics [leap-frog integrator]; md-vv = md using velocity verlet; sd = stochastic dynamics) dt= 0.002; Time-step (ps) nsteps= 5; Number of steps to run (0.002 * 5 = 100 ps) ; Parameters controlling output writing nstxout= 1; Write coordinates to output .trr file every 2 ps nstvout= 1000; Write velocities to output .trr file every 2 ps nstenergy= 1000; Write energies to output .edr file every 2 ps nstlog= 1000; Write output to .log file every 2 ps ; Parameters describing neighbors searching and details about interaction calculations ns_type= grid; Neighbor list search method (simple, grid) nstlist= 5; Neighbor list update frequency (after every given number of steps) rlist= 1.2; Neighbor list search cut-off distance (nm) rlistlong = 1.4 rcoulomb= 1.2; Short-range Coulombic interactions cut-off distance (nm) rvdw= 1.2; Short-range van der Waals cutoff distance (nm) pbc= xyz; Direction in which to use Perodic Boundary Conditions (xyz, xy, no) vdwtype = switch rvdw_switch = 0.8 ; Parameters for treating bonded interactions continuation= no; Whether a fresh start or a continuation from a previous run (yes/no) constraint_algorithm = LINCS; Constraint algorithm (LINCS / SHAKE) constraints= h-bonds ; Which bonds/angles to constrain (all-bonds / hbonds / none / all-angles / h-angles) lincs_iter= 1; Number of iterations to correct for rotational lengthening in LINCS (related to accuracy) lincs_order= 4; Highest order in the expansion of the constraint coupling matrix (related to accuracy) ; Parameters for treating electrostatic interactions coulombtype= PME; Long range electrostatic interactions treatment (cut-off, Ewald, PME) pme_order= 4; Interpolation order for PME (cubic interpolation is represented by 4) fourierspacing= 0.16; Maximum grid spacing for FFT grid using PME (nm) ; Temperature coupling parameters tcoupl= v-rescale; Modified Berendsen thermostat using velocity rescaling tc-grps= Protein POPCSOL_CL; Define groups to be coupled separately to temperature bath tau_t= 0.10.10.1; Group-wise coupling time constant (ps) ref_t= 310 310310; Group-wise reference temperature (K) ; Pressure coupling parameters pcoupl= no ; Under NVT conditions pressure coupling is not done ; Miscellaneous control parameters ; Dispersion correction DispCorr= EnerPres; Dispersion corrections for Energy and Pressure for vdW cut-off ; Initial Velocity Generation gen_vel= yes; Generate velocities from Maxwell distribution at given temperature gen_temp= 310; Specific temperature for Maxwell distribution (K) gen_seed= -1; Use random seed for velocity generation (integer; -1 means seed is calculated from the process ID number) ; Centre of mass (COM) motion removal relative to the specified groups nstcomm= 1; COM removal frequency (steps) comm_mode= Linear; Remove COM translation (linear / angular / no) comm_grps= Protein_POPC SOL_CL; COM removal relative to the specified groups Any suggestions please? Yes, the
Re: [gmx-users] LINCS WARNING - Protein-Membrane-system
Thanks. Sincerely, Shima - Original Message - From: Justin Lemkul jalem...@vt.edu To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users gmx-users@gromacs.org Cc: Sent: Tuesday, January 1, 2013 7:27 PM Subject: Re: [gmx-users] LINCS WARNING - Protein-Membrane-system On 1/1/13 10:53 AM, Shima Arasteh wrote: If I tell you that I changed the constraints and now the NVT is running, would that be ok? However I don't know the scientific reason of this incident! But I bring you the EM.mdp as follow: define = -DSTRONG_POSRES integrator = steep ; Algorithm (steep = steepest descent minimization) emtol = 100.0 ; Stop minimization when the maximum force 100.0 kJ/mol/nm emstep = 0.01 ; Energy step size nsteps = 5 ; Maximum number of (minimization) steps to perform ; Parameters describing how to find the neighbors of each atom and how to calculate the interactions nstlist = 1 ; Frequency to update the neighbor list and long range forces ns_type = grid ; Method to determine neighbor list (simple, grid) rlist = 1.2 ; Cut-off for making neighbor list (short range forces) coulombtype = PME ; Treatment of long range electrostatic interactions rcoulomb = 1.2 ; Short-range electrostatic cut-off rvdw = 1.2 ; Short-range Van der Waals cut-off pbc = xyz ; Periodic Boundary Conditions And the NVT.mdp as follow (after change of all-bond constraint to h-bond): title = NVT equilibration for dimer-POPC - CHARMM36 define = -DPOSRES ; Protein is position restrained (uses the posres.itp file information) ; Parameters describing the details of the NVT simulation protocol integrator = md ; Algorithm (md = molecular dynamics [leap-frog integrator]; md-vv = md using velocity verlet; sd = stochastic dynamics) dt = 0.002 ; Time-step (ps) nsteps = 5 ; Number of steps to run (0.002 * 5 = 100 ps) ; Parameters controlling output writing nstxout = 1 ; Write coordinates to output .trr file every 2 ps nstvout = 1000 ; Write velocities to output .trr file every 2 ps nstenergy = 1000 ; Write energies to output .edr file every 2 ps nstlog = 1000 ; Write output to .log file every 2 ps ; Parameters describing neighbors searching and details about interaction calculations ns_type = grid ; Neighbor list search method (simple, grid) nstlist = 5 ; Neighbor list update frequency (after every given number of steps) rlist = 1.2 ; Neighbor list search cut-off distance (nm) rlistlong = 1.4 rcoulomb = 1.2 ; Short-range Coulombic interactions cut-off distance (nm) rvdw = 1.2 ; Short-range van der Waals cutoff distance (nm) pbc = xyz ; Direction in which to use Perodic Boundary Conditions (xyz, xy, no) vdwtype = switch rvdw_switch = 0.8 ; Parameters for treating bonded interactions continuation = no ; Whether a fresh start or a continuation from a previous run (yes/no) constraint_algorithm = LINCS ; Constraint algorithm (LINCS / SHAKE) constraints = h-bonds ; Which bonds/angles to constrain (all-bonds / hbonds / none / all-angles / h-angles) lincs_iter = 1 ; Number of iterations to correct for rotational lengthening in LINCS (related to accuracy) lincs_order = 4 ; Highest order in the expansion of the constraint coupling matrix (related to accuracy) ; Parameters for treating electrostatic interactions coulombtype = PME ; Long range electrostatic interactions treatment (cut-off, Ewald, PME) pme_order = 4 ; Interpolation order for PME (cubic interpolation is represented by 4) fourierspacing = 0.16 ; Maximum grid spacing for FFT grid using PME (nm) ; Temperature coupling parameters tcoupl = v-rescale ; Modified Berendsen thermostat using velocity rescaling tc-grps = Protein POPC SOL_CL ; Define groups to be coupled separately to temperature bath tau_t = 0.1 0.1 0.1 ; Group-wise coupling time constant (ps) ref_t = 310 310 310 ; Group-wise reference temperature (K) ; Pressure coupling parameters pcoupl = no ; Under NVT conditions pressure coupling is not done ; Miscellaneous control parameters ; Dispersion correction DispCorr = EnerPres ; Dispersion corrections for Energy and Pressure for vdW cut-off ; Initial Velocity Generation gen_vel = yes ; Generate velocities from Maxwell distribution at given temperature gen_temp = 310 ; Specific temperature for Maxwell distribution (K) gen_seed = -1 ; Use random seed for velocity generation
