[gmx-users] Problems when simulating a protein in its crystal matrix.
Mark Abraham
mark.abraham at anu.edu.au
Mon Oct 18 03:30:36 CEST 2010
Try a smaller integration timestep while you equilibrate. Set nstxout = 1 and look closely at the region that starts to break. Try without constraints. Alternatively, simplify/change the problem by (say) stripping all the crystal waters before adding, or solvating only one copy of the protein (to diagnose topology issues).
Mark
----- Original Message -----
From: Itamar Kass <itamar.kass at monash.edu>
Date: Monday, October 18, 2010 11:14
Subject: [gmx-users] Problems when simulating a protein in its crystal matrix.
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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> Hi All,
I wish to simulate a protein in its crystal form. The crystal is a triclinic box with a C2 symmetry. I have built the unit cell, which has 4 copies of the protein, and add some water on top of the ones in the pdb. Then minimized and run positional restrained MD followed by a non restrained MD. The system crashed after ~600ps reporting of LINCS errors.
>
> Now I have minimized it before running; I have checked the topology and could not find any error; I have also tried to run it in shake and the system crashed as well; I also run the system in NVT without any success.
I guess this is a symptom to something like pressure problems, PBC issues or bad topology, but I could not find it. I also looked for an isolated water molecule which might have caused it, without any success. So I hope someone else can come with the bright idea I don’t have.
The rate of water and protein is ~1 protein to 300 water molecules, In addition I add NaCl to neutralise the system and bring it to 0.1M concentration.
Also here is my mdp file:
integrator = md
dt = 0.002 ; ps !
nsteps = 2500000
; OPTIONS FOR BONDS
; Constrain control
constraints = all-bonds
; Do not constrain the start configuration
continuation = yes
; Type of constraint algorithm
constraint-algorithm = lincs
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 100000
nstvout = 100000
nstfout = 100000
; Output frequency and precision for xtc file
nstxtcout = 2500
xtc-precision = 1000
; Energy monitoring
energygrps = Protein
nstenergy = 1000
; NEIGHBORSEARCHING PARAMETERS
; nblist update frequency
nstlist = 5
; ns algorithm (simple or grid)
ns-type = Grid
; nblist cut-off
rlist = 0.8
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = Reaction-Field
rcoulomb = 1.4
epsilon_rf = 62
vdw-type = Cut-off
; cut-off lengths
rvdw-switch = 0
rvdw = 1.4
; Apply long range dispersion corrections for Energy and Pressure
DispCorr = no
; OPTIONS FOR WEAK COUPLING ALGORITHMS
; Temperature coupling
tcoupl = berendsen
; Groups to couple separately, time constant (ps) and reference temperature (K)
tc-grps = Protein solvent
tau-t = 0.1 0.1
ref-t = 300 300
; Pressure coupling
Pcoupl = no
Pcoupltype = isotropic
; Time constant (ps), compressibility (1/bar) and reference P (bar)
tau_p = 1.0
compressibility = 4.5e-5
ref_p = 1.0
; Do not generate velocities
gen_vel = no
; Center of mass control
nstcomm = 10000
; Periodic boundary conditions
pbc = xyz
; Mode for center of mass motion removal
comm-mode = Linear
; Groups for center of mass motion removal
comm-grps = system
> Thanks in advance,
> Itamar.
> -- > > > "In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut > > =========================================== > | Itamar Kass, Ph.D. > | Postdoctoral Research Fellow > | > | Department of Biochemistry and Molecular Biology > | Building 77 Clayton Campus > | Wellington Road > | Monash University, > | Victoria 3800 > | Australia > | > | Tel: +61 3 9902 9376 > | Fax: +61 3 9902 9500 > | E-mail: Itamar.Kass at monash.edu > ============================================ |
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