[gmx-users] Simulation terminated after 260 ns of simulation

[anu chandra]

Dear Gromcas users,

I have been carrying out a simulation of protein in POPC membrane.  After
the successful completion of about 260 ns, simulation terminated with the
following error.

***************************************************************
Reading checkpoint file 16md.cpt generated: Sun Jan 17 06:38:52 2016


Using 4 MPI processes
Using 6 OpenMP threads per MPI process

2 GPUs detected on host tesla68:
  #0: NVIDIA Tesla K20c, compute cap.: 3.5, ECC: yes, stat: compatible
  #1: NVIDIA Tesla K20c, compute cap.: 3.5, ECC: yes, stat: compatible

2 GPUs auto-selected for this run.
Mapping of GPUs to the 2 PP ranks in this node: #0, #1

Non-default thread affinity set probably by the OpenMP library,
disabling internal thread affinity

WARNING: This run will generate roughly 5432 Mb of data
starting mdrun 'Title'
133000000 steps, 266000.0 ps (continuing from step 120500000, 241000.0 ps).

NOTE: Turning on dynamic load balancing


-------------------------------------------------------
Program gmx_mpi, VERSION 5.0.5
Source code file: /tmp/gromacs-5.0.5/src/gromacs/mdlib/pme.c, line: 754

Fatal error:
35983 particles communicated to PME rank 2 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.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

********************************************************************


I am using the following input parameters for simulation. I also used
flat-bottom position restrain  during simulation.

******************************************************************
define                  = -DPOSRES -DMD -DPOSRES_POT
;
integrator              = md
dt                      = 0.002
nsteps                  = 500000
tinit                   = 0
init-step               = 0
;
nstlog                  = 1000
nstxout                 = 20000
nstvout                 = 20000
nstfout                 = 20000
nstcalcenergy           = 100
nstenergy               = 1000
nstxout-compressed      = 4000
compressed-x-grps       = System
;
cutoff-scheme           = Verlet
nstlist                 = 20
rlist                   = 1.2
coulombtype             = pme
rcoulomb                = 1.2
vdwtype                 = Cut-off
vdw-modifier            = Force-switch
rvdw_switch             = 1.0
rvdw                    = 1.2
;
pbc                     = xyz
;
tcoupl                  = Nose-Hoover
tc_grps                 = Protein POPC K_CL_SOL
tau_t                   = 1.0    1.0     1.0
ref_t                   = 305.0    305.0    305.0
;
pcoupl                  = Parrinello-Rahman
pcoupltype              = semiisotropic
tau_p                   = 5.0     5.0
compressibility         = 4.5e-5  4.5e-5
ref_p                   = 1.0     1.0
;
constraints             = h-bonds
constraint_algorithm    = LINCS
continuation            = yes
;
nstcomm                 = 100
comm_mode               = linear
comm_grps               = Protein_POPC K_CL_SOL
;
refcoord_scaling        = com

**********************************************************************************

I just wonder why Gromcas detected an improper system equilibration after
250 ns of simulation, though the system looks fine. Can anybody help me to
get rid off the error here.


Many thanks in advance

Anu