[gmx-users] MDRUN errors

[Rahul Karyappa]

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
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


Where am I going wrong? Please tell me. Thanking you in advance.


Rahul Karyappa

NCL, Pune







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