[gmx-users] Error in Energy Minimization

[Sunny]

Hi Tsjerk,

The system has 1 protein (118 atoms) and 256 DPPC lipids (12800 atoms) 
without solvent. The box size is 6.125, 12.5, 9.5 nm. The make_ndx output is 
as follows. I can run l-bfgs on the structure.

Analysing residue names:
Opening library file 
/usr/local/packages/gromacs/g_3.3.1/share/gromacs/top/aminoacids.dat
There are:   256      OTHER residues
There are:    12    PROTEIN residues
There are:     0        DNA residues
Analysing Protein...
Analysing Other...

  0 System              : 12918 atoms
  1 Protein             :   118 atoms
  2 Protein-H           :    89 atoms
  3 C-alpha             :    12 atoms
  4 Backbone            :    36 atoms
  5 MainChain           :    49 atoms
  6 MainChain+Cb        :    58 atoms
  7 MainChain+H         :    63 atoms
  8 SideChain           :    55 atoms
  9 SideChain-H         :    40 atoms
10 Prot-Masses         :   118 atoms
11 Non-Protein         : 12800 atoms
12 DPP                 : 12800 atoms
13 Other               : 12800 atoms

George

>From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] Error in Energy Minimization
>Date: Tue, 16 Jan 2007 13:31:15 +0100
>
>Hi George,
>
>You didn't mention whether this was with or without solvent. This is
>probably due to an error in your starting structure, and I advice to
>check it carefully. Also, if you're running in solvent, check your
>box.
>
>>Step=   57, Dmax= 4.3e-03 nm, Epot= -1.79963e+23 Fmax=         inf, atom= 
>>2
>
>The only thing I don't really get is this potential energy. Can you
>give more details about your system? Type of molecules, size, etc?
>
>Cheers,
>
>Tsjerk
>
>--
>Tsjerk A. Wassenaar, Ph.D.
>Junior UD (post-doc)
>Biomolecular NMR, Bijvoet Center
>Utrecht University
>Padualaan 8
>3584 CH Utrecht
>The Netherlands
>P: +31-30-2539931
>F: +31-30-2537623
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