[gmx-users] MDRUN errors

[leafyoung81-group at yahoo.com]

--- Rahul Karyappa <r.karyappa at ncl.res.in> wrote:

> 
> Dear all,
> 
>     I created .gro and .top files for my structure
> with
> 48 repeat units of polymer surrounded by sodium ions
> and water. First I
> carried out energy minimization by steepest descents
> and then I ran MD
> for 2ps (40 steps). It runs upto 40 steps  properly
> and then it
2/40 = 0.05ps = 50fs. Time step is too big for MD.
Normally, 1 to 2fs.
> starts giving errors as follows:
> 
> starting mdrun 'Protein'
> 
> 1000 steps,      2.0 ps.
> 
> 
> step 40, remaining runtime:    23
> s             
> Warning: 1-4 interaction between 294 and 297 at
> distance larger than 1
> nm
> 
> These are ignored for the rest of the simulation
> 
> turn on -debug for more information
> 
> step 50, remaining runtime:    18
> s             
> Wrote pdb files with previous and current
> coordinates
> 
> Wrote pdb files with previous and current
> coordinates
> 
> 
> Back Off! I just backed up step55.pdb to
> ./#step55.pdb.1#
> 
> Wrote pdb files with previous and current
> coordinates
> 
> 
> Back Off! I just backed up step56.pdb to
> ./#step56.pdb.1#
> 
> Wrote pdb files with previous and current
> coordinates
> 
> ...
> 
> Back Off! I just backed up step60.pdb to
> ./#step60.pdb.1#
> 
> Wrote pdb files with previous and current
> coordinates
> 
> Fatal error: ci = -2147483648 should be in 0 .. 1330
> [FILE nsgrid.c, LINE 218]
> 
> 
> Also when I ran steepest descents the messages I got
> were as follows:
> 
> 
> Step=   44, Dmax= 1.2e-04 nm, Epot= -1.10077e+05
> Fmax= 2.65510e+03, atom= 725
> 
> Step=   52, Dmax= 1.1e-06 nm, Epot= -1.10077e+05
> Fmax= 3.00823e+03, atom= 8860
> 
> Stepsize too small, or no change in energy.
> 
> Converged to machine precision,
> 
> but not to the requested precision Fmax < 1000
> 
> 
> 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 steep.trr to
> ./#steep.trr.1#
> 
> 
> Back Off! I just backed up steepout.gro to
> ./#steepout.gro.1#
> 
> 
> Steepest Descents converged to machine precision in
> 53 steps,
> 
> but did not reach the requested Fmax < 1000.
> 
> Potential Energy  = -1.1007694e+05
> 
> Maximum force     =  2.6551050e+03 on atom 725
> 
> Norm of force     =  1.0160128e+05
> 
>
This is not an error. Try other em methods or proceed
to equilibrium.

> Where am I going wrong? Please tell me. Thanking you
> in advance.
> 
> 
> Rahul Karyappa
> 
> NCL, Pune
> 
> 
> 
> 
> 
> 
> 
>
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