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.
David
On 6/25/06, MURAT CETINKAYA <[EMAIL PROTECTED]> 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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