[gmx-users] free energy and fatal error

David Mobley dmobley at gmail.com
Mon Jun 26 18:28:29 CEST 2006

Which version of GROMACS are you using?

If you can create two tpr files generated from the same structures and
mdp files except with free_energy=yes in one and free_energy=no in the
other, and only one of these exhibits the behavior you're describing
when run, I suggest submitting these to Bugzilla.

I vaguely remember having a problem like this myself once before, but
it turned out I hadn't minimized properly or some such. It sounds like
you don't think that's what's going on though.


On 6/25/06, MURAT CETINKAYA <cetinkayam at psu.edu> wrote:
> Hi,
> 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
> thanks
> Murat CETINKAYA, M.Sc.
> 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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