[gmx-users] mdrun failure

[fatemeh ramezani]

 Hi dear gmx-usersI am simulating gold surface- protein interaction by 
GOLP-CHARMM forcefield. after 30 ps equilibration, I started mdrun with some 
freeze atoms in gold surface and NVT ensemble in temp=300 k, but when mdrun 
starts, temperature reaches to 5.50769e+05. md.mdp file containe:
title    = gold
cpp   = cpp
include   = 

; RUN CONTROL PARAMETERS
integrator   = md 
comm_mode  = Linear
;nstcomm   =  1
;comm_grps   = Protein  Non-protein 
;nstcalcenergy = 1
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol   = 500.0
emstep    = 0.001
tinit  = 0.000
dt = 0.0005
nsteps  = 10

; OUTPUT CONTROL OPTIONS
nstxout = 3000
nstvout = 3000
nstfout  = 0
nstlog   = 1
nstenergy = 3000

; Output frequency and precision for xtc file
nstxtcout  = 3000
xtc-precision    = 3000



; NEIGHBORSEARCHING PARAMETERS
; Periodic boundary conditions: xyz (default), no (vacuum)
pbc  = xyz
periodic_molecules    = yes
; nblist cut-off    
rlist   = 1.10

; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = PME
r_coulomb    = 1.1
;pme_order   = 6
;fourierspacing   = 0.10
ewald_rtol    = 1e-06
ewald_geometry  = 3d

; Method for doing Van der Waals
vdw-type = switch
; cut-off lengths   
rvdw-switch   = 0.90
rvdw = 1.10

; OPTIONS FOR BONDS    
constraints   = none
constraint-algorithm  =  Lincs
lincs-order   = 8
lincs-iter   = 12
; Lincs will write a warning to the stderr if in one step a bond
; rotates over more degrees than
lincs-warnangle = 90

; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling  
Tcoupl    = Nose-Hoover
nhchainlength   = 1
; Groups to couple separately
tc-grps = Protein  SOL NA CL     slab AUC 
; Time constant (ps) and reference temperature (K)
tau-t    =  0.2 0.2 0.2 0.2 0.2  0.2
ref-t =  300 300 300 300 300 300

; Non-equilibrium MD stuff
freezegrps    = slab
freezedim = Y Y Y

Can anyone help me to solve this problem?thank you in advance

Fatemeh Ramezani
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[gmx-users] mdrun failure

[fatemeh ramezani]

Hi dear gmx-users

Iwant to simulate gold surface - protein interaction by GOLP-CHARMM 
forcefield.In md step, after 7 ps , without any reason mdrun failed. md.mdp 
contains:

 title                   = gold

cpp                     =cpp

include                 = 

 ;RUN CONTROL PARAMETERS

integrator              = md 

 ;ENERGY MINIMIZATION OPTIONS

emtol                   = 500.0

emstep                  = 0.001

tinit                   = 0.000

dt                      =0.001

nsteps = 10

 ;OUTPUT CONTROL OPTIONS

nstxout                 = 3000

nstvout                 = 3000

nstfout                 = 0

nstlog                  = 1

nstenergy               = 3000

 ;Output frequency and precision for xtc file

nstxtcout               = 3000

xtc-precision           = 3000

 ;NEIGHBORSEARCHING PARAMETERS

;Periodic boundary conditions: xyz (default), no (vacuum)

pbc                     =xyz

periodic_molecules      = yes

rlist                   = 1.10

 ;OPTIONS FOR ELECTROSTATICS AND VDW

;Method for doing electrostatics

coulombtype             = PME

r_coulomb                = 1.1

ewald_rtol              = 1e-06

ewald_geometry          = 3d

 ;Method for doing Van der Waals

vdw-type                = switch

rvdw-switch             = 0.90

rvdw                    = 1.10

 ;OPTIONS FOR BONDS    

constraints             = h-bonds

constraint-algorithm    = Lincs

lincs-order             = 8

lincs-iter              = 12

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

;rotates over more degrees than

lincs-warnangle         = 90

 ;OPTIONS FOR WEAK COUPLING ALGORITHMS

;Temperature coupling  

Tcoupl                  = Nose-Hoover

nhchainlength = 1

;Groups to couple separately

tc-grps                 = Protein  Non-Protein

;Time constant (ps) and reference temperature (K)

tau-t                   = 0.2 0.2

ref-t                   = 310 310

 ;Non-equilibrium MD stuff

freezegrps              = slab

freezedim               = Y Y Y

 

mdrun command is:

 nohup mdrun -smd.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.logis:

 Step          Time         Lambda

          7460        7.46000       0.0

    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

    KineticEn.   Total Energy  Conserved En.    Temperature Pressure(bar)

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

   Constr.rmsd

   1.15453e-01

 The last line ofnohup.out is:

  Changing nstlist from 10to 40, rlist from 1.1 to 1.1

 Using 1 MPI thread

Using 3 OpenMP threads

Applying core pinningoffset 1

Setting the maximumnumber of constraint warnings to -1

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

 Back Off! I just backedup traj_comp.xtc to ./#traj_comp.xtc.22#

 Back Off! I just backedup md3.edr to ./#md3.edr.20#

starting mdrun 'Proteinin water'

10 steps,   100.0 ps.

 Can you help me toprevent from mdrun failing?

Thank you very much

 
 Fatemeh Ramezani
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