[gmx-users] segmentation fault with unusually high temperature and energy values

[Sahithya S Iyer]

Hi gmx users,

I am trying to set up a membrane protein system. The protein has to be at a
specific location of the heterogeneous bilayer patch (hence i cannot use
inflateGRO.py) to set up the system. I used vmd to place the protein and
remove overlapping lipid ("within 3 of protein"). There are no overlapping
molecules in my system now.

When i try to energy minimize this system, the simulation crashes with
segmentation error. The log files shows abnormally high energy and
temperature values -

Grid: 25 x 24 x 7 cells
Large VCM(group rest): 219789.21875, -46415.75391, -69344.71094, Temp-cm:
2.55463e+12
   Energies (kJ/mol)
           Bond       G96Angle  Improper Dih.        LJ (SR)   Coulomb (SR)
    9.44989e+07    1.67042e+05    1.96681e+04    1.59212e+18   -2.29853e+05
 Position Rest.      Potential    Kinetic En.   Total Energy    Temperature
    3.58499e+02    1.59212e+18    2.35242e+35    2.35242e+35    3.00779e+32
 Pressure (bar)   Constr. rmsd
    4.60453e+32    5.67792e+13

When i visualize the trajectroy, in the second frame, the atoms are
scattered all over outside the box !
I have run the lipid patch and protein system (separately) individually and
it runs fine without any error.

Can someone please tell me where i am going wrong..