[gmx-users] Re: Potential energy positive. Can be?

Mark Abraham Mark.Abraham at anu.edu.au
Fri Aug 17 00:07:32 CEST 2007

Eudes Fileti wrote:
> Dear Mark,
> Thank you for the link. It was useful.
> I have choosen the volume using the editiconf by setting
> the experimental density for toluene. In fact, my potential
> can be wrong.
> So, I asked you if you would have a topology or an equilibrated box for the
> toluene, since this could be very useful to me.
> (but my text was not understandable, sorry).

Well I don't, but you can try generating an equilibrated box yourself 
using some NPT after NVT, as the link suggested.

To generate a topology try the resources suggested there, or get 
literature describing the force field you want to use and work by 
analogy from benzene (as you did). If you follow the rules by which the 
force field was developed, then by doing so you can have some confidence 
of generating a reliable physical model. Even then, you won't always be 
able to reproduce an experimental density, but if it's far wrong you can 
use that to search for a problem in your setup.


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