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

[Mark Abraham]

Hi,

Position restraints and volume changes are not a happy combination, and
even less happy with large time steps. I would look closely at such
quantities in your output that suggest you were doing something that isn't
intrinsically stable. One option is to start the equilibration with a small
time step, e.g. 0.1 fs and no constraints. If I knew my starting protein
configuration was really special and wanted to start from it after
equilibration, I'd strongly consider equilibrating, and then imposing some
restraint to fix anything that made me unhappy.

Mark

On Tue, Jan 19, 2016 at 12:53 PM anu chandra <anu80125 at gmail.com> wrote:

> 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
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