[gmx-users] grompp 5.1.3 chokes on multiple tau_p for semiisotropic pcoupltype
Mark Abraham
mark.j.abraham at gmail.com
Tue Jul 26 21:29:21 CEST 2016
Hi,
Yes that's now the correct behaviour, as a side effect of fixing a bug
where you could pass 0.8 to an integral parameter and it would silently
interpret it as 0...
Mark
On Tue, 26 Jul 2016 20:50 David Dotson <dldotson at asu.edu> wrote:
> Ah, I see now. tau-p only gets a single value, but compressibility and
> ref-p get a value for each of the two directions. Doing this yields no
> errors. Thanks Justin!
>
> David
>
>
> On 07/26/2016 11:45 AM, Justin Lemkul wrote:
> >
> >
> > On 7/26/16 2:39 PM, David Dotson wrote:
> >> 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.
> >>
> >
> > Semiisotropic coupling only ever accepted one single value. grompp
> silently accepted multiple values and ignored all but the first. As of
> 5.1.2 (IIRC) this was corrected. So what grompp is doing now is correct
> and what it was doing before was the actual bug.
> >
> > -Justin
> >
>
> --
> David L. Dotson * david.dotson at asu.edu
> Beckstein Lab
> Center for Biological Physics
> Arizona State University
>
> becksteinlab.physics.asu.edu
>
> --
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