[gmx-users] mdrun failed

[fatemeh ramezani]

 Hi dear gmx-usersI want to simulate gold surface - proteininteraction by GOLP-CHARMM forcefield. In md step, after 7 ps , without anyreason mdrun failed. md.mdp contains:





title                   = gold

cpp                     = cpp

include                 =

 

; RUN CONTROL PARAMETERS

integrator              = md

;comm_mode              = Linear

;nstcomm =   1

;comm_grps             = Protein  non-Protein

;nstcalcenergy  = 1

; ENERGY MINIMIZATIONOPTIONS

; Force tolerance andinitial step-size

emtol                   = 500.0

emstep                  = 0.001

tinit                   = 0.000

dt                      = 0.001

nsteps                                 = 100000

 

; OUTPUT CONTROL OPTIONS

nstxout                 = 3000

nstvout                 = 3000

nstfout                 = 0

nstlog                  = 1

nstenergy               = 3000

;nsttcouple = 5

; Output frequency andprecision for xtc file

nstxtcout               = 3000

xtc-precision           = 3000

 

 

 

; NEIGHBORSEARCHINGPARAMETERS

; Periodic boundaryconditions: xyz (default), no (vacuum)

pbc                     = xyz

periodic_molecules      = yes

; nblistcut-off      

rlist                   = 1.10

 

; OPTIONS FORELECTROSTATICS AND VDW

; Method for doingelectrostatics

coulombtype             = PME

r_coulomb                = 1.1

;pme_order               = 6

;fourierspacing                   = 0.10

ewald_rtol              = 1e-06

ewald_geometry          = 3d

 

; Method for doing Vander Waals

vdw-type                = switch

; cut-offlengths     

rvdw-switch             = 0.90

rvdw                    = 1.10

 

; OPTIONS FORBONDS  

constraints             = all-bonds

constraint-algorithm    = Lincs

lincs-order             = 8

lincs-iter              = 12

; Lincs will write awarning to the stderr if in one step a bond

; rotates over moredegrees than

lincs-warnangle         = 90

 

; OPTIONS FOR WEAKCOUPLING ALGORITHMS

; Temperature coupling

Tcoupl                  = Nose-Hoover

nhchainlength                  = 1

; Groups to coupleseparately

tc-grps                 =Protein            Non-Protein

; Time constant (ps) andreference temperature (K)

tau-t                   = 0.2 0.2

ref-t                   = 310 310

 

; Non-equilibrium MDstuff

freezegrps              = slab

freezedim               = Y Y Y

 

Fatemeh Ramezani

 

mdrun command is:

 nohup mdrun -s md.tpr-o md.trr -c md.pdb -g md.log -e md.edr -nt 3 -dd 1 -pin on -pinoffset 1  &

 

the last line of md.log is:

 Step           Time         Lambda

           7460        7.46000        0.00000

 

   Energies (kJ/mol)

            U-B    Proper Dih. Improper Dih.      CMAP Dih.          LJ-14

    5.39081e+04    1.47221e+04    3.15826e+03   -1.85050e+03    1.80904e+04

     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.      Potential

    2.97824e+05    2.17254e+12   -6.91585e+06    3.01612e+04    2.17254e+12

    Kinetic En.   Total Energy Conserved En.    TemperaturePressure (bar)

    7.71065e+14    7.73237e+14    9.41950e+16    2.61554e+11    2.41578e+12

   Constr. rmsd

    1.15453e-01

 

The last line of nohup.out is:

 Changing nstlist from10 to 40, rlist from 1.1 to 1.1

 Using 1 MPI thread

Using 3 OpenMP threads

Applying core pinning offset 1

Setting the maximum number of constraint warnings to -1

 

Back Off! I just backed up fws_md3.trr to ./#fws_md3.trr.20#

 Back Off! I justbacked up traj_comp.xtc to ./#traj_comp.xtc.22#

 Back Off! I justbacked up md3.edr to ./#md3.edr.20#

starting mdrun 'Protein in water'

100000 steps,    100.0ps.

 

Can you help me to prevent from mdrun failing?

Thank you very much

Fatemeh Ramezani