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

[Guo, Yanan]

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.



Any help and suggestion are appreciated.

Thank you very much!



Greetings

Yanan