On 7/9/12 9:40 AM, [email protected] wrote:
Hi Justin,
okey then I will try it with this timestep.
No it is not my goal to do a NVE. I already had temperature coupling
options in my .mdp file but on the blowing up side was written "you are
using inappropriate temperature coupling" so I thought that that might be
the reason and deleted it from my .mdp file.
Temperature coupling in itself is not the source of the problem, but what is
stated on the wiki is that inappropriate use of it can lead to instability. The
settings below look fine. I think your biggest problem is the large timestep.
-Justin
I had the following temperature coupling options:
tcoupl = V-rescale
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 298 298
pcoupl = no
Thank you for your answer.
Eva
On 7/9/12 9:25 AM, [email protected] wrote:
Hi everybody,
I want to do a md for a protein with a membrane around it.
I already minimised the energy of the protein.
Output of the minimization:
^MStep= 812, Dmax= 1.4e-06 nm, Epot= -7.59283e+05 Fmax= 3.59781e+02,
atom= 1653
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 10
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
writing lowest energy coordinates.
Steepest Descents converged to machine precision in 813 steps,
but did not reach the requested Fmax < 10.
Potential Energy = -7.5928356e+05
Maximum force = 3.6197971e+02 on atom 1653
Norm of force = 2.6517429e+00
In my eyes this output was okey so I went on with the md.
And here I get the error:
Fatal error:
A charge group moved too far between two domain decomposition steps
This usually means that your system is not well equilibrated
I already read the error page for this error and also the blowing up
page
but I still do not know what to do now.
My .mdp file for the md runs looks like this:
define = -DPOSRES
integrator = md
dt = 0.005
This timestep is huge. Even with constraints, you probably can't exceed 2
fs
stably (0.002 ps).
nsteps = 2000
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstxtcout = 0
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
Are here any optinos which can cause the error?
In the absence of temperature and/or pressure coupling, the ensemble
you're
trying to simulate is NVE, which is very tricky to get stabilized.
http://www.gromacs.org/Documentation/Terminology/NVE
If you're not going for an NVE ensemble, you need several adjustments in
the
.mdp file. See any basic tutorial for examples of how to simulate other
ensembles, if this is your goal.
-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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--
========================================
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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