[gmx-users] high temperature during mdrun

fatemeh ramezani fr_750 at yahoo.com
Wed May 24 15:12:37 CEST 2017




  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 and mdrun fails. 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      = 100000

; 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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