[gmx-users] Re: Positive Potential Energy after equilibration

[Satish Kamath]

I've refined the charge distribution.
   nr      type  resnr resid  atom  cgnr   charge-  prodrg (NEW)     	mass
     1        OA     1  F09     OAD     1   -0.117 (-0.596)  		15.9994   
     2         H     1  F09     HAD     1    0.027 (+0.469)		1.0080   
     3         C     1  F09     CAC     1    0.078 (+0.274)		12.0110   
     4       CR1     1  F09     CAF     1   -0.005 (-0.390)		12.0110   
     5        HC     1  F09     HAF     1    0.014 (+0.195)	   	1.0080   
     6         C     1  F09     CAH     1   -0.014 (+0.104)		12.0110   
     7       CR1     1  F09     CAI     1   -0.006 (-0.197) 		12.0110   
     8        HC     1  F09     HAI     1    0.014 (+0.140)  		1.0080   
     9       CR1     1  F09     CAK     1   -0.005 (-0.139) 		12.0110   
    10        HC     1  F09     HAK     1    0.014 (+0.139)		1.0080   
    11       CR1     1  F09     CAL     2   -0.006 (-0.139)		12.0110   
    12        HC     1  F09     HAL     2    0.014 (+0.139) 		1.0080   
    13       CR1     1  F09     CAJ     2   -0.005 (-0.197)		12.0110   
    14        HC     1  F09     HAJ     2    0.014 (+0.140)		1.0080   
    15         C     1  F09     CAG     2   -0.014 (+0.104)		12.0110   
    16       CR1     1  F09     CAA     2   -0.005 (-0.390)		12.0110   
    17        HC     1  F09     HAA     2    0.013 (+0.195)		1.0080   
    18         C     1  F09     CAB     2    0.078 (+0.274) 		12.0110   
    19        OA     1  F09     OAE     2   -0.116 (-0.594) 		15.9994   
    20         H     1  F09     HAE     2    0.027 (+0.469)		1.0080
The ones in the bracket are the new charges applied. These are from the
Automated Topology Builder which does the QM calculations. They seemed more
appropriate as they match with the ones on p-cresol in the paper. I did not
modify the bond parameters from PRODRG as suggested by the paper. The
potential energy has reduced and is arnd 1.5e+04 but is still positive. Can
I get some help with this? Thank you for all the help in advance. :)

Satish Kamath
IISc Bangalore

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