[gmx-users] Regarding em potential energy coming possitive

[Swagata Patra]

Hello everyone,

I am facing a problem in energy minimization step. I am not sure if the
system is energy minimized or not. After completing the em, I am getting
the following message:
Reached the maximum number of steps before reaching Fmax < 1

Steepest Descents did not converge to Fmax < 1 in 100001 steps.
Potential Energy  = -9.38185842721980e+06
Maximum force     =  4.73530543550372e+02 on atom 1694
Norm of force     =  1.11096437377417e+00
But when I am calculating the potential energy getting the following
message:
Energy                      Average   Err.Est.       RMSD  Tot-Drift
-------------------------------------------------------------------------------
Potential                   121.811    1.9e+06        nan   -2017.89
 (kJ/mol)

Potential energy should come negative. But here its too high.
One more thing that I want to tell is, in my protein pdb file there is gap
between amino acids(like G229 then H412). That's why in topology file I am
getting two chains.
Please suggest me what could be the problem?
-- 
Swagata Patra
M.Tech (Biotech)
JRF
IIT Guwahati