[gmx-users] MD run error

[Kushal Seth]

Hi again !

Thanks a lot for your help. its a great learning experience since am new to
GROMACS.
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

Kushal






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
> 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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