[gmx-users] grompp 5.1.3 chokes on multiple tau_p for semiisotropic pcoupltype
Justin Lemkul
jalemkul at vt.edu
Tue Jul 26 20:45:12 CEST 2016
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
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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