[gmx-users] energy minimization

[Dongsheng Zhang]

Dear All,

I use hyperChem to build a peptoid molecule (40 units). When I do energy
minimization, I get this error message:


Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =          200
Warning: 1-4 interaction between 904 and 927 at distance larger than 1
nm
These are ignored for the rest of the simulation
turn on -debug for more information
Fatal error: ci = -2147483648 should be in 0 .. 7799 [FILE nsgrid.c,
LINE 218]


The following information is from em.log:

           Step           Time         Lambda
              0        0.00000        0.00000

Fatal error: ci = -2147483648 should be in 0 .. 7799 [FILE nsgrid.c,
LINE 218]

According to David's answer to such a similar question, this problem
results from bad contacts in the molecules. Could anyone tell me how to
check where are the bad contacts, so I can remove them manually? Thanks!



-- 
Dongsheng Zhang <dong at pampas.chem.purdue.edu>