[gmx-users] free energy and fatal error

MURAT CETINKAYA cetinkayam at psu.edu
Mon Jun 26 05:53:40 CEST 2006


I am trying to calculate solvation free energy of a non-standard residue and I
have problems in vacuum runs.

I defined a dummy atom for every single atom in the molecule (0 charge and
non-bonded parameters) and I input every single bonded interaction values
manually (in order to prevent any errors resulting from that).

I minimized my molecule with l-bfgs and steep. If do free energy = no, I can do
my NVT run in vacuo without any problems. However, when I set:

free_energy              = yes
init_lambda              = 0.0
delta_lambda             = 0
sc_alpha                 = 0.5
sc-power                 = 1.0
sc-sigma                 = 0.3

I get the following error:
step 0Warning: 1-4 interaction between 21 and 23 at distance larger than 2.4 nm
These are ignored for the rest of the simulation
turn on -debug for more information
Fatal error: ci = -2147483648 should be in 0 .. 63 [FILE nsgrid.c, LINE 218]

As I said, every bonded interaction value is entered manually (A = B values) and
structure seems minimized.

Any ideas appreciated
BioNanoMaterials Group,
Dept. of Engr. Science and Mechanics,
The Pennsylvania State University,
University Park, PA 16802
office: (814) 863 9967
web: www.personal.psu.edu/muc176

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