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" <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: "Discussion list for GROMACS users" <gmx-users@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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