On 5/24/17 8:52 AM, fatemeh ramezani wrote:
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 = 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
Do not do this.
http://www.gromacs.org/Documentation/Terminology/Thermostats
; 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
Your system is blowing up. Follow the standard advice at
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
as well as the cautionary notes about using freezing and required energy group
exclusions at
http://manual.gromacs.org/documentation/2016.3/user-guide/mdp-options.html#non-equilibrium-md
-Justin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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