[gmx-users] MD run error
kushalseth at gmail.com
Thu Apr 13 02:36:14 CEST 2006
Hi again !
Thanks a lot for your help. its a great learning experience since am new to
Well I have made a membrane and i have put two water boxes on top of the
membrane.These three structures were combined in to one and i wanted to run
energy minimization on the resulting structure.
I errors i got earlier have vanised when i added the ; table-extension = 3.8
in to my mdp file (thry trial and error).
i would like to know if this is OK, secondly i get the following outputs
after 116 steps
"Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 100
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.
Back Off! I just backed up em.trr to ./#em.trr.9#
Back Off! I just backed up emout.pdb to ./#emout.pdb.9#
Steepest Descents converged to machine precision in 117 steps,
but did not reach the requested Fmax < 100.
Potential Energy = 5.4069402e+08
Maximum force = 3.0060948e+06 on atom 14374
Norm of force = 4.0884328e+07"
Below is the copy of my mdp file :
; User spoel (236)
; Wed Nov 3 17:12:44 1993
; Input file
title = Yo
cpp = /usr/bin/cpp
constraints = none
integrator = steep
; ENERGY MINIMIZATION OPTIONS =
; Force tolerance and initial step-size =
emtol = 100
emstep = 0.005
; Max number of iterations in relax_shells =
niter = 20
; Frequency of steepest descents steps when doing CG =
nstcgsteep = 1000
dt = 0.002 ; ps !
nsteps = 5000 ; total 10 ps = 10/0.002.
nstcomm = 1
nstxout = 250
nstvout = 1000
nstfout = 0
nstxtcout = 50
nstlog = 100
nstenergy = 100
nstlist = 10
ns_type = grid
coulombtype = PME
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
DispCorr = EnerPres
table-extension = 3.8
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc-grps = POP CHO OCH SOL
tau_t = 0.1 0.1 0.1 0.1
ref_t = 300 300 300 300
; Energy monitoring
energygrps = POP CHO OCH SOL
; Isotropic pressure coupling is now on
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 0.5 0.5 0.5
compressibility = 4.5e-5
ref_p = 1.0
; Generate velocites is off at 300 K.
gen_vel = no
gen_temp = 300.0
gen_seed = 173529
Thanks in advance
On 4/11/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Kushal Seth wrote:
> > Hi all !
> > I am running a MD simulation and i got
> You appear to be trying to do an energy minimization, which although
> often able to be done by the same code as molecular dynamics, is
> inherently non-dynamical. Hence it's unwise to confuse matters by
> referring to one as "MD". See section 1 of the gromacs manual.
> > "Warning: 1-4 interaction between 1 and 6 at distance 1.102 which is
> > larger than the 1-4 table size 1.000 nm
> > These are ignored for the rest of the simulation
> > This usually means your system is exploding,
> > if not, you should increase table-extension in your mdp file"
> It's probably right about that. Look at 1 and 6 in the initial structure
> and see what you think they should do. Then look at the output of the EM
> and see what they have done. This may suggest where the problem lies.
> > and then EM process goes and terminates at 26 th steps saying that
> > "Stepsize too small, or no change in energy.
> > Converged to machine precision,
> > but not to the requested precision Fmax < 100
> > 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 26 steps,
> > but did not reach the requested Fmax < 100.
> > Potential Energy = -6.0066115e+23
> > Maximum force = 1.8847882e+25 on atom 2502
> > Norm of force = 5.5707627e+25".
> > I have tried changing the sizes and pressure couplings.Thats does not
> Pressure coupling can only be applied to a dynamical simulation, so this
> cannot help at all.
> Check your input structure, your topology, the output structure and your
> input .mdp file. If the former are all OK and you can't see anything
> wrong with the .mdp file, include it in a message here.
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