[gmx-users] MDRUN errors

[leafyoung81-group at yahoo.com]

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

> 
> 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
Perhaps you have constraints defined in the topology.
You may proceed to equilibration.

> 
> 
> 
> 
> -- 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
> >
> >
> >
> >
> >
> >
> >
> >
>
*****************************************************************
> > This email is virus free by TrendMicro Inter Scan
> > Security Suite.
> >
>
*****************************************************************>
> _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the
> > list. Use the
> > www interface or send it to
> gmx-users-request at gromacs.org.
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the
> list. Use the
> www interface or send it to
> gmx-users-request at gromacs.org.
>
*****************************************************************
> This email is virus free by TrendMicro Inter Scan
> Security Suite.
>
*****************************************************************
> 
> 
>
*****************************************************************
> This email is virus free by TrendMicro Inter Scan
> Security Suite.
>
*****************************************************************