[gmx-users] Energies rising

[David van der Spoel]

Sampo Karkola wrote:
> Hi, Bharat and thanks for the answer.
> 
> now I'm running an md simulation with the ternary complex (protein, 
> cofactor, ligand) where the potential energy has risen and stabilised to 
> a certain level, at least for the first 300 ps. I understand that the 
> potential energy can rise and I'll be happy if the md finishes nicely. 
> However, I'm confused with the difference between my earlier 
> simulations, in which every time the potential energy decreased in the 
> beginning of the simulation and stabilised. I managed to perform an md 
> for the cofactor NADP (NDPP topology) where the potential energy 
> decreased using a different mdp file than earlier, so I think the 
> problem is in the input, as suggested by David van der Spoel.
> 
> I'll try to dig in to the parametrisation of the mdrun.
> 
You may also want to reflect on your input. Sometimes you can see the 
energy go down, for instance when you have a system at low density that 
contracts, and sometimes it can go up, e.g. when you start at 0 K and 
increase the T. If you generate velocities in grompp the rise should not 
at all be so high. I don't think the force field is the problem here.

-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++