[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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