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

[Justin A. Lemkul]

On 6/12/12 4:13 AM, Satish Kamath wrote:
> 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. :)
>

Those charges certainly do look better.  How long are your simulations?  It may 
take quite a while for your system to rearrange and equilibrate appropriately.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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