[gmx-users] grompp 5.1.3 chokes on multiple tau_p for semiisotropic pcoupltype
David Dotson
dldotson at asu.edu
Tue Jul 26 20:39:49 CEST 2016
Greetings,
Using gromacs 5.1.3's `gmx grompp` on the MDP file below (also attached) with `gmx grompp -c start.gro -f premd.mdp -p system.top -n index.ndx`:
; Gromacs mdp file
include = -I. -I.. -I../top
define =
integrator = sd
tinit = 0.0
dt = 0.0001
nsteps = 1000000
nstxout = 50000
nstvout = 50000
nstfout = 0
; Output frequency for energies to log file and energy file
nstlog = 500
nstenergy = 100
; Output frequency and precision for xtc file
nstxout-compressed = 500
compressed-x-precision = 1000
; center of mass motion removal
comm-mode = Linear ; translation only
nstcomm = 1000 ; frequency
comm-grps = SYSTEM
; Selection of energy groups
;energygrps = __main__ __environment__
; Overall cutoff scheme to use (Verlet = GPU)
cutoff-scheme = Verlet ; gromacs 5.x CHARMM
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 20 ; frequency
; ns algorithm (simple or grid)
ns_type = grid ; performance choice
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic_molecules = no
; nblist cut-off
;rlist = 1.2 ; gromacs 5.x CHARMM; Piggot suggested 1.4
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME ; gromacs 5.x CHARMM
rcoulomb-switch = 0
rcoulomb = 1.2 ; gromacs 5.x CHARMM must equal rvdw for Verlet
coulomb-modifier = potential-shift-verlet
; Relative dielectric constant for the medium and the reaction field
epsilon_r = 1
epsilon_rf = 1
; Method for doing Van der Waals
vdwtype = cutoff ; gromacs 5.x CHARMM
rvdw-switch = 1.0 ; gromacs 5.x CHARMM
rvdw = 1.2 ; gromacs 5.x CHARMM
vdw-modifier = force-switch ; gromacs 5.x CHARMM
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = no ; gromacs 5.x CHARMM Piggot
; Seperate tables between energy group pairs
energygrp_table =
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12 ; Piggot
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4 ; Piggot
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = yes
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = no ; for langevin dynamics
tc-grps = PROTEIN LIPIDS SOLVENT
tau_t = 0.1 0.1 0.1 ; must be > 20*.04 with Verlet
ref_t = 310 310 310 ; for us
; Pressure coupling
pcoupl = parrinello-rahman ; Piggot
pcoupltype = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 5.0 5.0 ; Piggot
compressibility = 4.6e-5 4.6e-5
ref_p = 1.0 1.0 ; Piggot
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = All
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen-temp = 310
gen_seed = 622794
; OPTIONS FOR BONDS
constraints = h-bonds ; gromacs 5.x CHARMM
constraint-algorithm = Lincs
lincs-order = 4
lincs-iter = 2 ; Piggot
; Distance restraints type: No, Simple or Ensemble
; (use simple for runs with distant restraints)
disre = No
; Free energy control stuff
free-energy = yes
sc-alpha = 0.5
sc-power = 1
sc-sigma = 0.3
init-lambda-state = 5
fep-lambdas = 0.0 0.025 0.05 0.075 0.1 0.125 0.15 0.175 0.2 0.225 0.25 0.275 0.3 0.325 0.35 0.375 0.4 0.425 0.45 0.475 0.5 0.525 0.55 0.575 0.6 0.625 0.65 0.675 0.7 0.725 0.75 0.775 0.8 0.825 0.85 0.875 0.9 0.925 0.95 0.975 1.0
;nstdhdl = 20
calc-lambda-neighbors = -1
dhdl-derivatives = yes
dhdl-print-energy = potential
separate-dhdl-file = no
we get an error giving:
ERROR 1 [file /nfs/homes4/dldotson/Projects/Transporters/NapA/SYSTEMS/ionbinding/na/if/restrained_to_repulsion/production1/res2rep_state_5_x1/setup/preproduction/premd.mdp, line 117]:
Right hand side '5.0 5.0' for parameter 'tau_p' in parameter file is not
a real value
Back Off! I just backed up /nfs/homes4/dldotson/Projects/Transporters/NapA/SYSTEMS/ionbinding/na/if/restrained_to_repulsion/production1/res2rep_state_5_x1/setup/preproduction/premdout.mdp to /nfs/homes4/dldotson/Projects/Transporters/NapA/SYSTEMS/ionbinding/na/if/restrained_to_repulsion/production1/res2rep_state_5_x1/setup/preproduction/#premdout.mdp.12#
-------------------------------------------------------
Program gmx grompp, VERSION 5.1.3
Source code file: /nfs/homes4/dldotson/Sysadmin/install/gromacs/source/gromacs-5.1.3/src/gromacs/gmxlib/readinp.c, line: 287
Fatal error:
There was 1 error in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
A few questions
1. Is grompp failing to parse multiple values now, or has something changed in how these should be given for things like semiisotropic pressure coupling?
2. If this is a legitimate bug in grompp, are there any recommended workarounds?
3. If there are no workarounds for getting grompp under gromacs 5.1.3 to properly parse multiple values, is it safe to use grompp from 5.1.1 (which did not have this problem) to build the TPR file and then use 5.1.3 for executing MD / everything else? Is there anything that could go very wrong with doing this?
I should note that giving only a single value for things like tau_p in an attempt to get past this issue give:
ERROR 1 [file /nfs/homes4/dldotson/Projects/Transporters/NapA/SYSTEMS/ionbinding/na/if/restrained_to_repulsion/production1/res2rep_state_5_x1/setup/preproduction/premd.mdp, line 117]:
Pressure coupling not enough values (I need 2)
so at present it's not clear to me how one might use nonisotropic pressure coupling in gromacs 5.1.3.
Thanks!
David
--
David L. Dotson * david.dotson at asu.edu
Beckstein Lab
Center for Biological Physics
Arizona State University
becksteinlab.physics.asu.edu
-------------- next part --------------
; Gromacs mdp file
include = -I. -I.. -I../top
define =
integrator = sd
tinit = 0.0
dt = 0.0001
nsteps = 1000000
nstxout = 50000
nstvout = 50000
nstfout = 0
; Output frequency for energies to log file and energy file
nstlog = 500
nstenergy = 100
; Output frequency and precision for xtc file
nstxout-compressed = 500
compressed-x-precision = 1000
; center of mass motion removal
comm-mode = Linear ; translation only
nstcomm = 1000 ; frequency
comm-grps = SYSTEM
; Selection of energy groups
;energygrps = __main__ __environment__
; Overall cutoff scheme to use (Verlet = GPU)
cutoff-scheme = Verlet ; gromacs 5.x CHARMM
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 20 ; frequency
; ns algorithm (simple or grid)
ns_type = grid ; performance choice
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic_molecules = no
; nblist cut-off
;rlist = 1.2 ; gromacs 5.x CHARMM; Piggot suggested 1.4
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME ; gromacs 5.x CHARMM
rcoulomb-switch = 0
rcoulomb = 1.2 ; gromacs 5.x CHARMM must equal rvdw for Verlet
coulomb-modifier = potential-shift-verlet
; Relative dielectric constant for the medium and the reaction field
epsilon_r = 1
epsilon_rf = 1
; Method for doing Van der Waals
vdwtype = cutoff ; gromacs 5.x CHARMM
rvdw-switch = 1.0 ; gromacs 5.x CHARMM
rvdw = 1.2 ; gromacs 5.x CHARMM
vdw-modifier = force-switch ; gromacs 5.x CHARMM
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = no ; gromacs 5.x CHARMM Piggot
; Seperate tables between energy group pairs
energygrp_table =
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12 ; Piggot
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4 ; Piggot
ewald_rtol = 1e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = yes
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = no ; for langevin dynamics
tc-grps = PROTEIN LIPIDS SOLVENT
tau_t = 0.1 0.1 0.1 ; must be > 20*.04 with Verlet
ref_t = 310 310 310 ; for us
; Pressure coupling
pcoupl = parrinello-rahman ; Piggot
pcoupltype = semiisotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 5.0 ; Piggot
compressibility = 4.6e-5
ref_p = 1.0 ; Piggot
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = All
; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel = yes
gen-temp = 310
gen_seed = 622794
; OPTIONS FOR BONDS
constraints = h-bonds ; gromacs 5.x CHARMM
constraint-algorithm = Lincs
lincs-order = 4
lincs-iter = 2 ; Piggot
; Distance restraints type: No, Simple or Ensemble
; (use simple for runs with distant restraints)
disre = No
; Free energy control stuff
free-energy = yes
sc-alpha = 0.5
sc-power = 1
sc-sigma = 0.3
init-lambda-state = 5
fep-lambdas = 0.0 0.025 0.05 0.075 0.1 0.125 0.15 0.175 0.2 0.225 0.25 0.275 0.3 0.325 0.35 0.375 0.4 0.425 0.45 0.475 0.5 0.525 0.55 0.575 0.6 0.625 0.65 0.675 0.7 0.725 0.75 0.775 0.8 0.825 0.85 0.875 0.9 0.925 0.95 0.975 1.0
;nstdhdl = 20
calc-lambda-neighbors = -1
dhdl-derivatives = yes
dhdl-print-energy = potential
separate-dhdl-file = no
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