zeppelin zeppelin wrote:
Dear GROMACS users,
I only begin to work with gromacs and now have some problems with tetra
protein.
I used AMBER force field and made several changes (in ffamber.rtp,
specbond.dat, ffamber99bon.itp) to create an isopeptide bonds between
monomers.
Minimization and equilibration (NPT and NVT) were OK.
But in MD (1.2 ns) I met a problem:
__________________________________________________________________
Step 241687, time 483.374 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms nan, max inf (between atoms 2431 and 2432)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2431 2432 90.0 0.1244 inf 0.1229
2428 2430 113.1 0.1010 64418817769472.0000 0.1010
2428 2429 105.7 0.1010 65196395593728.0000 0.1010
.........................................
t = 483.374 ps: Water molecule starting at atom 57549 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Segmentation fault
________________________________________________________________________
When I looked on step241686c.pdb in pymol, I found, that GLY that form
one of isopeptide bonds exploded (it's atoms were far from the water box).
I saw that a lot of people have a close problem, but usually they have
it on the first steps. Also in my case minimization and equilibration
were OK. I note some letters with the close problem, but I don't
understand what to start with in my case. I kindly ask you to give me an
idea or a link to a letter with the best solution.
LINCS errors have many causes, and as such, there is no universal solution. The
normal advice for solving this problem is as follows:
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
I suspect with nstxout = 1000 you should have plenty of frames to watch at the
point where the system becomes unstable. Looking at a single .pdb file from the
crash will not show you how it happened; it just shows you what the result of
the unstable system was. It sounds to me like whatever parameters you're using
for your isopeptide bond are not stable, but you should decide that for yourself
based on what you see in the trajectory.
Simulation is based on tutorial: "Lysozyme in Water. Justin Lemkul"
Note that the .mdp files I provide are for OPLS-AA, and may not be universally
applicable. I make this caveat clear in the summary of the tutorial. You may
have to change some of the parameters (particularly cutoffs, nstlist, time step,
etc) to be compatible with AMBER.
-Justin
Thanks,
Yulian
HISTORY
/gromacs-4.0.5/bin/pdb2gmx -f 3ALB_AMBER.pdb -o processed.gro -water
tip3p -missing -merge
/gromacs-4.0.5/bin/editconf -f processed.gro -o newbox.gro -c -d 1.0
-bt cubic
/gromacs-4.0.5/bin/genbox -cp newbox.gro -cs spc216.gro -o solv.gro
-p topol.top
/gromacs-4.0.5/bin/grompp -f ions.mdp -c solv.gro -p topol.top -o
ions.tpr
/gromacs-4.0.5/bin/genion -s ions.tpr -o solv.gro -p topol.top -pname
Na+ -np 24
/gromacs-4.0.5/bin/grompp -f minim.mdp -c solv.gro -p topol.top -o
em.tpr
/gromacs-4.0.5/bin/mdrun -v -deffnm em
vmd em.gro
/gromacs-4.0.5/bin/g_energy -f em.edr -o potential.xvg
xmgrace potential.xvg
/gromacs-4.0.5/bin/grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr
/gromacs-4.0.5/bin/mdrun -v -deffnm nvt
/gromacs-4.0.5/bin/g_energy -f nvt.edr
xmgrace nvt.edr
xmgrace energy.xvg
/gromacs-4.0.5/bin/grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p
topol.top -o npt.tpr
/gromacs-4.0.5/bin/mdrun -v -deffnm npt
vmd npt.gro
/gromacs-4.0.5/bin/g_energy -f npt.edr -o pressure.xvg
xmgrace pressure.xvg
/gromacs-4.0.5/bin/g_energy -f npt.edr -o density.xvg
xmgrace density.xvg
/gromacs-4.0.5/bin/grompp -f md.mdp -c npt.gro -t npt.cpt -p
topol.top -o md_2ns.tpr
/gromacs-4.0.5/bin/mdrun -v -deffnm md_2ns
____________________________________________________________________
md.mdp
title = AMBER Ub_tetra48
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 600000 ; 2 * 500000 = 1000 ps, 1 ns
dt = 0.002 ; 2 fs
; Output control
nstxout = 1000 ; save coordinates every 2 ps
nstvout = 1000 ; save velocities every 2 ps
nstxtcout = 1000 ; xtc compressed trajectory output every 2 ps
nstenergy = 1000 ; save energies every 2 ps
nstlog = 1000 ; update log file every 2 ps
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more
accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each
group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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