[gmx-users] segementation fault- water molecule can not be settled- free mdrun error (repica exchange)

[Justin Lemkul]

On 1/12/14, 8:09 AM, Guo, Yanan wrote:
> Hello everyone,
>
> The procedure that I performed my MD simulation is as follows:
>
>
> 1.       pdb2gmx…
>
> 2.       editconf…
>
> 3.       genbox…
>
> 4.       genion…
>
> 5.       energy minimization…
>
> 6.       equilibration, to release the position restraints step by step
>
> firstly, equilibration in temperature phase (force on each atom in three axis is 1000)
>
> secondly, equilibration in pressure phase (force on each atom in three axis is 100)
>
> thirdly, equilibration in pressure phase (force on each atom in three axis is 10)
>
> 7.       replica exchange and simulated annealing (I would like to use this replica exchange or simulated annealing as the production MD simulation)
>
>
>
> Part of the error file of replica exchange:
>
>
>
> step 502: Water molecule starting at atom 29883 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
>
>
> step 502: Water molecule starting at atom 35217 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
>
>
> step 502: Water molecule starting at atom 36021 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
>
>
> step 502: Water molecule starting at atom 12588 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
>
>
> step 502: Water molecule starting at atom 24726 can not be settled.
>
> Check for bad contacts and/or reduce the timestep if appropriate.
>
> ……
>
> ……
>
> ……
>
> End of error message ***
>
> [ic2n113:43048] *** Process received signal ***
>
> [ic2n113:43048] Signal: Segmentation fault (11)
>
> [ic2n113:43048] Signal code: Address not mapped (1)
>
> [ic2n113:43048] Failing at address: 0x2aeb1fa73054
>
> [ic2n113:43067] *** Process received signal ***
>
> [ic2n113:43067] Signal: Segmentation fault (11)
>
> [ic2n113:43067] Signal code: Address not mapped (1)
>
> [ic2n113:43067] Failing at address: 0x2b2b1f0707d0
>
>
>
>
>
> The mdp file for replica exchange (the only difference among the replicas is the ref_t value)
>
> Run parameters
>
> integrator      = md
>
> nsteps          = 200000000
>
> dt              = 0.001
>
> ; Output control
>
> nstxout         = 0
>
> nstvout         = 0
>
> nstfout         = 0
>
> nstxtcout       = 10000
>
> nstenergy       = 10000
>
> nstlog          = 10000
>
> ; Bond parameters
>
> continuation    = yes
>
> constraint_algorithm = lincs
>
> constraints     = all-bonds
>
> lincs_iter      = 1
>
> lincs_order     = 4
>
> ; Neighborsearching
>
> ns_type         = grid
>
> nstlist         = 5
>
> rlist           = 1.0
>
> rcoulomb        = 1.0
>
> rvdw            = 1.0
>
> ; Electrostatics
>
> coulombtype     = PME
>
> pme_order       = 4
>
> fourierspacing  = 0.16
>
> ; Temperature coupling is on
>
> tcoupl          = V-rescale
>
> tc-grps         = Protein Non-Protein
>
> tau_t           = 0.1   0.1
>
> ref_t           = 300.00   300.00
>
> ; Pressure coupling is on
>
> pcoupl          = Parrinello-Rahman
>
> pcoupltype      = isotropic
>
> tau_p           = 2.0
>
> ref_p           = 1.0
>
> compressibility = 4.5e-5
>
> ; Periodic boundary conditions
>
> pbc             = xyz
>
> ; Dispersion correction
>
> DispCorr        = EnerPres
>
> ; Velocity generation
>
> gen_vel         = no
>
>
>
> What confuses me is that, there is no such error for the simulated annealing.
>
>
>
> There is no other difference between my sa.mdp and repl.mdp file except that sa.mdp contains the parameters of annealing.
>

REMD under an NPT ensemble can be unstable.  You may need to reduce your time 
step or otherwise change the pressure coupling settings for the runs to be 
stable.  If the temperature range includes very high temperatures, NPT simply 
may never be stable, because the exchanges between neighboring replicas will be 
problematic.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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