[gmx-users] MDRUN errors

[Rahul Karyappa]

Thank you for your kind reply. I tried conjugate gradient but it is not running. It gives error that it can't prform conjugate gradient minimization.
Rahul Karyappa




-- Original Message --
From: <leafyoung81-group at yahoo.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Date: Thu, 8 Sep 2005 05:41:31 -0700 (PDT)
Subject: Re: [gmx-users] MDRUN errors
--- 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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