On 9/18/12 8:58 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Okey,
now I tried it without any fixed residues. But still the energy after the
minimization is not very low and I still get the LINCS warnings.
The mdp file I use for the minimization looks like this:
define = -DPOSRES
Restraints during minimization generally restrict motion in the same way that
freezing does. Again, this is a potential barrier to sufficient minimization.
integrator = steep
emtol = 10
nsteps = 1500
nstenergy = 1
energygrps = System
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
rlist = 0.9
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
pbc = xyz
the mdp file for the md run looks like this:
define = -DPOSRES
integrator = md
dt = 0.001
nsteps = 5000
nstxout = 100
nstvout = 0
nstfout = 0
nstlog = 1000
nstxtcout = 500
nstenergy = 5
energygrps = Protein Non-Protein
nstcalcenergy = 5
nstlist = 10
ns-type = Grid
pbc = xyz
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
gen_vel = yes
gen_temp = 200.0
gen_seed = 9999
constraints = all-bonds
tcoupl = V-rescale
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 298 298
pcoupl = no
The output of the minimization run is:
Steepest Descents converged to machine precision in 15 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -7.9280412e+05
Maximum force = 1.0772942e+04 on atom 979
Norm of force = 9.6685356e+01
Note that this outcome is even worse than before. The maximum force is now over
10,000.
The output of the MD run is:
Step 1031, time 1.031 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001431, max 0.010707 (between atoms 976 and 979)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
976 979 81.6 0.1272 0.0970 0.0960
As you should expect. If you can't get a reasonable minimization, the MD will
always crash.
The atom 979 is the hydrogen atom on the phosphate. There has to be one
hydrogen atoms because it is protonated once. The other atom 976 is the
oxygen atom where the hydrogen atom is bound to.
The bounding parameters for this kind of binding were already there. I
didn't add them.
I already did it for another phosphorylation on another position in this
structure. And here I also got many LINCS errors. And again the problem is
the connection between the hydrogen atom and the oxygen atom.
But I do not understand why.
Remove all restraints/freezing/whatever in the .mdp file and try the EM again.
If it still does not converge to a reasonable value, then there are two
potential problems:
1. The topology is flawed and thus the structure cannot be run stably
2. The structure cannot accommodate phosphate in this location and due to
unresolvable clashes, the runs fail
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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