Hi again !
"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
Kushal
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 help.
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.
Mark
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