[gmx-users] Have your ever got a real NVE simulation (good energy conservation) in gromacs?

Erik Marklund erikm at xray.bmc.uu.se
Fri May 24 09:39:30 CEST 2013


I have achieved good energy conservation in NVE simulations. This was single proteins in the gas phase, using infinite cut-offs, constraints applied to hydrogens, 0.5 fs or 1.0 fs time steps, double precision and virtual sites if I'm not mistaken. We had problems with energy conservation for the first publication (Patriksson et al 2007, Biochemistry. The methods section states 1.0 fs, but that's a typo for we used 0.5 fs) for 1.0 fs time steps. For a second publication (Marklund et al 2009, PCCP) 1.0 fs worked fine, using a later gromacs version. In the first case we used SHAKE and in the later LINCS I think.

Hope that helps


On 23 May 2013, at 23:59, cyberjhon <cyberjhon at hotmail.com> wrote:

> Hi Guys
> I have been trying by all means to get a real good Energy conservation in
> NVE simulations using gromacs
> but it has been almost impossible for me. 
> I have tried many different combinations of Coulomb and VdW parameters and
> changed the cut off radius and nothing.
> 1. Have you ever obtained energy conservation in Gromacs?
> 2. Under what conditions ? for what system? 
> 2. Do you have a set of parameters that works to obtain energy conservation?
> if you can share with me the mdp file, I will appreciate it.
> My system is Human Papiloma Virus  virus-like particle T=1 inmersed in SPC
> water.
> Thanks
> John Michael Espinsoa Duran
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