Hey all,
Here is another error that I keep getting. I am trying to "speed up" my md runs with -heavyh and longer time steps. I don't get LINCS errors but I do get this...
Back Off! I just backed up prlog.log to ./#prlog.log.1#
Getting Loaded...
Reading file monomer_pr.tpr, VERSION 4.5.1 (single precision)
Starting 2 threads
Loaded with Money
Making 1D domain decomposition 2 x 1 x 1
Back Off! I just backed up pr.edr to ./#pr.edr.1#
starting mdrun 'Protein in water'
25000 steps, 100.0 ps.
step 900, will finish Mon Sep 27 18:19:07 2010imb F 18%
NOTE: Turning on dynamic load balancing
step 1600, will finish Mon Sep 27 18:18:42 2010vol 0.92 imb F 1%
A list of missing interactions:
LJC Pairs NB of 278 missing 1
exclusions of 6966 missing 1
-------------------------------------------------------
Program g4.5.1-mdrun, VERSION 4.5.1
Source code file: domdec_top.c, line: 173
Software inconsistency error:
Some interactions seem to be assigned multiple times
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
Some settings:
define = -DPOSRES
dt = 0.004
nsteps = 25000
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME ; = Cutoff
rcoulomb-switch = 0 ; = 0
rcoulomb = 0.9 ; = 1
; Relative dielectric constant for the medium and the reaction field
epsilon_r = 1 ; = 1
epsilon_rf = 1 ; = 1
; Method for doing Van der Waals
vdw-type = Cut-off ; = Cut-off
; cut-off lengths
rvdw-switch = 0 ; = 0
rvdw = 1 ; = 1
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = No ; = No
; Extension of the potential lookup tables beyond the cut-off
table-extension = 1 ; = 1
; Seperate tables between energy group pairs
energygrp_table = ; =
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12 ; = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0 ; = 0
fourier_ny = 0 ; = 0
fourier_nz = 0 ; = 0
; EWALD/PME/PPPM parameters
pme_order = 6 ; = 4
ewald_rtol = 1e-05 ; = 1e-05
ewald_geometry = 3d ; = 3d
epsilon_surface = 0 ; = 0
optimize_fft = yes ; = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = v-rescale ; = No
nsttcouple = -1 ; = -1
nh-chain-length = 10 ; = 10
; Groups to couple separately
tc-grps = RNA SOL ; =
; Time constant (ps) and reference temperature (K)
tau-t = 0.1 0.1 ; =
ref-t = 300 300 ; =
; Pressure coupling
Pcoupl = Parrinello-Rahman ; = No
Pcoupltype = Isotropic
nstpcouple = -1 ; = -1
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau-p = 1 ; = 1
compressibility = 4.5e-5 ; =
ref-p = 1.0 ; =
; Scaling of reference coordinates, No, All or COM
refcoord_scaling = No ; = No
; Random seed for Andersen thermostat
andersen_seed = 815131 ; = 815131
gen-vel = yes ; = no
gen-temp = 300 ; = 300
gen-seed = 173529 ; = 173529
constraints = all-bonds
Any help would be appreciated. It also seems to be intermittent as I have 21 identical runs (with different lambda values) and some work and some don't. It also changes every time I run them.
Thank you,
TJ Mustard
Email: musta...@onid.orst.edu
-- 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
