[gmx-users] unstable system
Justin Lemkul
jalemkul at vt.edu
Sat May 11 17:16:09 CEST 2013
On 5/11/13 2:12 AM, Shima Arasteh wrote:
> Hi,
>
>
> The commands are as this:
>
> EM:
>
> minim.mdp :
>
> 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 = 50000 ; 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)
> rlistlong = 1.4
> 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
> vdwtype = switch
> rvdw_switch = 1.0
> pbc = xyz ; Periodic Boundary Conditions
>
>
> #grompp -f minim.mdp -c minim_npt_9_mod.pdb -p topol.top -o minim_10.tpr
> # mpirun -np 32 mdrun_mpi -deffnm minim_10 -v
>
> Steepest Descents converged to Fmax < 100 in 5865 steps
> Potential Energy = -1.5278298e+06
> Maximum force = 7.5562675e+01 on atom 71284
> Norm of force = 2.8630490e+00
>
This looks reasonable. If you're using constraints later on, I would suggest
minimizing again with those same constraints before proceeding.
>
>
> NVT:
>
> nvt.mdp:
>
> title = NVT equilibration for dimer-POPC-water - CHARMM36
> define
> = -DPOSRES_LIPID -DPOSRES ; P headgroups of POPC and 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 = 0.001 ; Time-step (ps)
> nsteps = 2000000 ; Number of steps to run (0.001 * 20000000 = 2000 ps)
>
> ; Parameters controlling output writing
> nstxout = 2000 ; 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 = 1.0
> ; 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 Water_and_ions ; Define groups to be coupled separately to temperature bath
> tau_t = 0.1 0.1 ; Group-wise coupling time constant (ps)
> ref_t = 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 (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 Water_and_ions ; COM removal relative to the specified groups
> refcoord_scaling = com
>
> REPEAT NVT over minim_10:
>
> #grompp -f nvt.mdp -c minim_10.gro -p topol.top -n index_mod_2.ndx -o nvt_10.tpr
> #mpirun -np 42 mdrun_mpi -deffnm nvt_10 -v
>
>
> NVT passed successfully.
>
> NPT
>
> ;NPT equlibration Dimer-POPC-Water - CHARMM36
> define = -DPOSRES
> integrator = md ; leap-frog integrator
> nsteps =1000000 ; 1 * 1000000 = 1000 ps
> dt = 0.001 ; 1 fs
> ; Output control
> nstxout = 2000 ; save coordinates every 0.4 ps
> nstvout = 2000 ; save velocities every 0.2 ps
> nstenergy = 1000 ; save energies every 0.2 ps
> nstlog = 1000 ; update log file every 0.2 ps
>
> continuation = yes ; first dynamics run
> constraint_algorithm = lincs ; holonomic constraints
> constraints = h-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 = 1.2 ; short-range neighborlist cutoff (in nm)
> rlistlong = 1.4
> rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
> rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
> vdwtype = switch
> rvdw_switch = 1.0
> ; 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 = Nose-Hoover ; modified Berendsen thermostat
> tc-grps = Protein_POPC Water_and_ions ; two coupling groups - more accurate
> tau_t = 0.5 0.5 ; time constant, in ps
> ref_t = 310 310 ; reference temperature, one for each group, in K
> pcoupl = Berendsen ; no pressure coupling in NVT
> pcoupltype = semiisotropic
> tau_p = 4
> ref_p = 1.01325 1.01325
> compressibility = 4.5e-5 4.5e-5
>
> ; Periodic boundary conditions
> pbc = xyz ; 3-D PBC
> ; Dispersion correction
> DispCorr = no ; account for cut-off vdW scheme
Why are you turning off dispersion correction after you used it previously?
> ; Velocity generation
> gen_vel = no ; assign velocities from Maxwell distribution
> ;gen_temp = 310 ; temperature for Maxwell distribution
> ;gen_seed = -1 ; generate a random seed
> nstcomm = 1
> comm_mode = Linear
> comm_grps = Protein_POPC Water_and_ions
>
> ;
> refcoord_scaling = com
>
> #grompp -f npt.mdp -c nvt_10.gro -t nvt_10.cpt -p topol.top -n index_mod_2.ndx -o npt_10.tpr -pp -maxwarn 1
> #mpirun -np 32 mdrun_mpi -deffnm npt_10
>
> NPT passed successfully.
>
> MD
> md.mdp :
>
> integrator
> = md ; Algorithm ("md" = molecular dynamics [leap-frog
> integrator]; "md-vv" = md using velocity verlet; sd = stochastic
> dynamics)
> dt = 0.001 ; Time-step (1fs)
> nsteps = 500000 ; Number of steps to run (0.001 * 500000 = 0.5 ns)
>
> ; Parameters controlling output writing
> nstxout = 1 ; Write coordinates to output .trr file every 10 ps
> nstvout = 5000 ; Write velocities to output .trr file every 10 ps
> nstenergy = 1000 ; Write energies to output .edr file every 2 ps
> nstlog = 5000 ; 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 = 1.0
> ; Parameters for treating bonded interactions
> continuation = yes ; Whether a fresh start or a continuation from a previous run (yes/no)
> constraint_algorithm = LINCS ; Constraint algorithm (LINCS / SHAKE)
> constraints = all-bonds ; Which bonds/angles to constrain (all-bonds / hbonds / none / all-angles / h-angles)
Now you're switching the constraint type. You minimized with no constraints,
equilibrated with restraints on h-bonds, and now you're constraining all bonds.
That's probably the source of your problem right there. Some bond between
heavy atoms was never minimized properly, was equilibrated happily because its
bond wasn't restrained, and now you're trying to constrain it. Hence your
simulation immediately fails.
Remain consistent throughout your workflow. If you want to constrain all bonds,
do so during every step.
-Justin
> 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 = Nose-Hoover ; Modified Berendsen thermostat using velocity rescaling
> tc-grps = Protein_POPC Water_and_ions ; Define groups to be coupled separately to temperature bath
> tau_t = 0.5 0.5 ; Group-wise coupling time constant (ps)
> ref_t = 310 310 ; Group-wise reference temperature (K)
>
> ; Pressure coupling parameters
> pcoupl = Parrinello-Rahman ; Pressure coupler used under NPT conditions
> pcoupltype = semiisotropic ; Isotropic scaling in the x-y direction, independent of the z direction
> tau_p = 2.0 ; Coupling time constant (ps)
> ref_p = 1.01325 1.01325 ; Reference pressure for coupling, x-y, z directions (bar)
> compressibility = 4.5e-5 4.5e-5 ; Isothermal compressibility (bar^-1)
>
> ; Miscellaneous control parameters
> ; Dispersion correction
> DispCorr = EnerPres ; Dispersion corrections for Energy and Pressure for vdW cut-off
> ; Initial Velocity Generation
> gen_vel = no ; Velocity is read from the previous run
> ; 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 Water_and_ions ; COM removal relative to the specified groups
>
>
>
> #grompp -f md.mdp -c npt_10.gro -t npt_10.cpt -p topol.top -n index_MOD_2.ndx -o md_0_1.tpr
> #mdrun -deffnm md_0_1
>
>
> The output of mdrun is :
>
> starting mdrun 'Protein'
> 500000 steps, 500.0 ps.
>
> Step 0, time 0 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.001763, max 0.045803 (between atoms 4724 and 4722)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 4722 4719 32.0 0.1603 0.1585 0.1530
> 4721 4719 31.3 0.1111 0.1118 0.1111
> 4720 4719 32.8 0.1111 0.1114 0.1111
> 4718 4716 31.3 0.1111 0.1112 0.1111
> 4717 4716 33.6 0.1111 0.1117 0.1111
> step 0
> Step 1, time 0.001 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.649109, max 18.927546 (between atoms 4720 and 4719)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 231 233 32.1 0.1546 0.1965 0.1538
> 233 236 48.5 0.1531 0.2415 0.1510
> 233 235 43.4 0.1119 0.1590 0.1111
> 233 234 41.6 0.1121 0.1563 0.1111
> 236 242 61.6 0.1455 0.1731 0.1440
> 237 239 83.6 0.1376 0.3084 0.1370
> 242 243 43.3 0.1384 0.1339 0.1368
> 243 245 78.5 0.1387 0.2446 0.1375
> 243 244 69.1 0.1092 0.1129 0.1080
> 239 241 76.4 0.1383 0.3464 0.1375
> 239 240 72.8 0.0985 0.1805 0.0976
> 241 247 85.6 0.1380 1.6944 0.1368
> 241 242 73.4 0.1411 0.3049 0.1400
> 247 249 87.8 0.1385 1.6202 0.1375
> 247 248 87.8 0.1091 1.4854 0.1080
> 4722 4719 65.6 0.1585 2.2749 0.1530
> 4721 4719 69.0 0.1118 1.8299 0.1111
> 4720 4719 71.2 0.1114 2.2140 0.1111
> 4725 4722 172.5 0.1585 0.4254 0.1530
> 4724 4722 117.0 0.1162 0.4249 0.1111
> 4723 4722 119.8 0.1150 0.4255 0.1111
> 4727 4725 81.1 0.1115 0.1977 0.1111
> 4726 4725 73.1 0.1116 0.2040 0.1111
> 4730 4728 40.7 0.1112 0.0589 0.1111
> 4728 4729 33.3 0.1112 0.0617 0.1111
> 245 249 84.6 0.1381 0.5203 0.1375
> 245 246 84.0 0.1084 0.3678 0.1080
> 249 250 82.4 0.1084 0.3844 0.1080
> 4707 4704 38.1 0.1531 0.1972 0.1530
> 4710 4707 57.9 0.1533 0.3614 0.1530
> 4709 4707 43.7 0.1112 0.1560 0.1111
> 4708 4707 45.0 0.1111 0.1572 0.1111
> 4713 4710 148.7 0.1575 0.3961 0.1530
> 4712 4710 81.6 0.1113 0.3191 0.1111
> 4711 4710 83.5 0.1114 0.3239 0.1111
> 4715 4713 129.1 0.1157 0.2442 0.1111
> 4714 4713 140.8 0.1148 0.3025 0.1111
> 4719 4716 109.1 0.1565 2.5635 0.1530
> 4718 4716 51.0 0.1112 1.1100 0.1111
> 4717 4716 53.9 0.1117 1.0950 0.1111
>
> Step 1, time 0.001 (ps) LINCS WARNING
> relative constraint deviation after LINCS:
> rms 0.005509, max 0.469113 (between atoms 4728 and 4729)
> bonds that rotated more than 30 degrees:
> atom 1 atom 2 angle previous, current, constraint length
> 233 236 30.2 0.1531 0.1485 0.1510
> 4728 4729 32.1 0.1112 0.0590 0.1111
> 4728 4730 39.2 0.1112 0.0561 0.1111
> 4725 4727 81.0 0.1115 0.1850 0.1111
> 4725 4726 72.6 0.1116 0.1915 0.1111
> 4722 4725 169.8 0.1585 0.4552 0.1530
> 4722 4724 116.2 0.1162 0.4645 0.1111
> 4722 4723 118.2 0.1150 0.4643 0.1111
> 4719 4722 66.4 0.1585 2.2611 0.1530
> 4719 4721 68.2 0.1118 1.7639 0.1111
> 4719 4720 71.0 0.1114 2.1695 0.1111
> 4716 4719 111.2 0.1565 2.5385 0.1530
> Wrote pdb files with previous and current coordinates
> Warning: 1-4 interaction between 4719 and 4726 at distance 2.217 which is larger than the 1-4 table size 2.200 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
>
> -------------------------------------------------------
> Program mdrun, VERSION 4.5.5
> Source code file: /home/abuild/rpmbuild/BUILD/gromacs-4.5.5/src/mdlib/pme.c, line: 538
>
> Fatal error:
> 2
> particles communicated to PME node 4 are more than 2/3 times the
> cut-off out of the domain decomposition cell of their charge group in
> dimension x.
> This usually means that your system is not well equilibrated.
>
> Would you please give me your suggestions?
>
>
> Sincerely,
> Shima
>
>
> ----- Original Message -----
> From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
> To: Justin Lemkul <jalemkul at vt.edu>; "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Cc:
> Sent: Wednesday, May 8, 2013 7:53 PM
> Subject: Re: [gmx-users] unstable system
>
> Yes, all steps were completed successfully.
> About your tips, OK sir.
>
> I' m going to go through the minimization and NVT and NPT again. Lets get my result, then will post the exact commands.
>
> Thanks for your suggestions.
>
>
>
> Sincerely,
> Shima
>
>
> ----- Original Message -----
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc:
> Sent: Wednesday, May 8, 2013 5:07 PM
> Subject: Re: [gmx-users] unstable system
>
>
>
> On 5/8/13 2:35 AM, Shima Arasteh wrote:
>> OK.
>>
>> 1. Exact commands given in the preparation protocol (EM and equilibration)
>>
>> EM:
>> # grompp -f minim.mdp -c input.gro -p topol.top -o minim.tpr
>> #mdrun -deffnm minim
>>
>> NVT:
>> #grompp -f nvt.mdp -c em.gro -p topol.top -n index.ndx -o nvt.tpr
>> #mdrun -deffnm nvt -v
>>
>> NPT:
>> # grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -n index.ndx -o npt.tpr
>> # mdrun_mpi -deffnm npt
>>
>>
>> *** Next removed some disturbing water molecules, so edited topol file and made a new index file index_mod_2.ndx:
>> Ran a new EM:
>> # grompp -f npt.mdp -c npt_mod.gro -p topol.top -o npt_minim.tpr
>> # mdrun -deffnm npt_minim
>>
>>
>> Ran a new NPT:
>> # grompp -f npt.mdp -c npt_minim.gro -p topol.top -n index_mod_2.ndx -o npt.tpr
>> # mdrun_mpi -deffnm npt
>>
>> I repeated the NPT the same as above in 3 steps:
>> a) restraints on lipid phosphorous and protein for 1 ns
>>
>> b) restraints on protein for 1ns
>>
>> c) restraint on protein with less force for 2 ns
>>
>
> All 3 of these steps complete successfully?
>
>>
>> MD:
>> # grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index_mod_2.ndx -o md_0_1.tpr
>> # mdrun -deffnm npt
>>
>
> There are a few discrepancies in the commands you have shown here, in particular
> naming differences between input and output file names. I ask for exact
> commands (not what you think you remember) for a very important reason - the
> diagnostic information you have provided (from the .log file) seems to indicate
> that the previous equilibrated state was not passed along to the MD step, so I
> suspect you've left out a checkpoint file somewhere or you have regenerated
> velocities by accident.
>
> As a tip, write all of your commands in a shell script and execute the script.
> Then, if something goes wrong and someone asks for exact commands, just copy and
> paste. I still can't tell if this is actually what you did.
>
>>
>> 3 particles communicated to PME node 2 are more than 2/3 times the cut -
>> off out of the domain decomposition cell of their charge group in
>> dimension y.
>> This usually means that your system is not well equilibrated.
>>
>>
>> 2. The .mdp files being used for all steps, most importantly NPT and MD
>>
>> npt.mdp:
>>
>> ;NPT equlibration Dimer-POPC-Water - CHARMM36
>> define = -DPOSRES
>> integrator = md ; leap-frog integrator
>> nsteps =1000000 ; 1 * 1000000 = 1000 ps
>> dt = 0.001 ; 1 fs
>> ; Output control
>> nstxout = 2000 ; save coordinates every 0.4 ps
>> nstvout = 2000 ; save velocities every 0.2 ps
>> nstenergy = 1000 ; save energies every 0.2 ps
>> nstlog = 1000 ; update log file every 0.2 ps
>>
>> continuation = yes ; first dynamics run
>> constraint_algorithm = lincs ; holonomic constraints
>> constraints = h-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 = 1.2 ; short-range neighborlist cutoff (in nm)
>> rlistlong = 1.4
>> rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
>> rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
>> vdwtype = switch
>> rvdw_switch = 1.0
>> ; 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 = Nose-Hoover ; modified Berendsen thermostat
>> tc-grps = Protein_POPC Water_and_ions ; two coupling groups - more accurate
>> tau_t = 0.5 0.5 ; time constant, in ps
>> ref_t = 310 310 ; reference temperature, one for each group, in K
>> pcoupl = Berendsen ; no pressure coupling in NVT
>> pcoupltype = semiisotropic
>> tau_p = 4
>> ref_p = 1.01325 1.01325
>> compressibility = 4.5e-5 4.5e-5
>>
>> ; Periodic boundary conditions
>> pbc = xyz ; 3-D PBC
>> ; Dispersion correction
>> DispCorr = no ; account for cut-off vdW scheme
>> ; Velocity generation
>> gen_vel = no ; assign velocities from Maxwell distribution
>> ;gen_temp = 310 ; temperature for Maxwell distribution
>> ;gen_seed = -1 ; generate a random seed
>> nstcomm = 1
>> comm_mode = Linear
>> comm_grps = Protein_POPC Water_and_ions
>> refcoord_scaling = com
>>
>>
>> md.mdp:
>>
>> title = Production run forGLC-Water-POPC system
>> define = -DPOSRES
>> ; Parameters describing the details of the NVT simulation protocol
>> integrator = md
>> dt = 0.001
>> nsteps = 2500000 ; Number of steps to run (0.002 * 2500000 = 5 ns)
>>
>> ; Parameters controlling output writing
>> nstxout = 1000 ; Write coordinates to output .trr file every 10 ps
>> nstvout = 2000 ; Write velocities to output .trr file every 10 ps
>> nstenergy = 1000 ; Write energies to output .edr file every 2 ps
>> nstlog = 5000 ; 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 = 1.0
>> ; Parameters for treating bonded interactions
>> continuation = yes ; Whether a fresh start or a continuation from a previous run (yes/no)
>> constraint_algorithm = LINCS ; Constraint algorithm (LINCS / SHAKE)
>> constraints = all-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 = Nose-Hoover ; Modified Berendsen thermostat using velocity rescaling
>> tc-grps = Protein_POPC Water_and_ions ; Define groups to be coupled separately to temperature bath
>> tau_t = 0.5 0.5 ; Group-wise coupling time constant (ps)
>> ref_t = 310 310 ; Group-wise reference temperature (K)
>>
>> ; Pressure coupling parameters
>> pcoupl = Parrinello-Rahman ; Pressure coupler used under NPT conditions
>> pcoupltype = semiisotropic ; Isotropic scaling in the x-y direction, independent of the z direction
>> tau_p = 2.0 ; Coupling time constant (ps)
>> ref_p = 1.01325 1.01325 ; Reference pressure for coupling, x-y, z directions (bar)
>> compressibility = 4.5e-5 4.5e-5 ; Isothermal compressibility (bar^-1)
>>
>> ; Miscellaneous control parameters
>> ; Dispersion correction
>> DispCorr = EnerPres ; Dispersion corrections for Energy and Pressure for vdW cut-off
>> ; Initial Velocity Generation
>> gen_vel = no ; Velocity is read from the previous run
>> ; 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 Water_and_ions ; COM removal relative to the specified groups
>>
>>
>
> I see no explanation as to why the run fails, aside from what I have said above.
>
> -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
========================================
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