[gmx-users] Re: NVE problems in gmx-users digest, Vol 1 #1174

David spoel at xray.bmc.uu.se
Tue Jan 6 20:29:01 CET 2004

On Tue, 2004-01-06 at 17:04, istvan at kolossvary.hu wrote:
> Hi, 

> A good way of testing energy conservation is using delta_E = log(1/N * 
> Sum|(Ei-E0)/E0|), see JCP 103, 1995, 9444-9459. Ei is the current total 
> energy, E0 is the initial total energy and N is the number of sample points 
> on the stretch of the trajectory considered. delta_E < -2.5 is indicative of 
> a stable constant energy simulation. With the above settings I was able to 
> keep delta_E below -2.5 for 33 ps. I guess this can be good or this can be 
> bad depending on your perspective. As far as I am concerned I am rather 
> disappointed that after only 33 ps the simulation should be considered 
> unstable. Can anybody comment on
> 1. Whether I missed something and even more conservative settings should be 
> used for NVE,
> 2. It concerns me a lot that we typically run hundreds or thousands of 
> picoseconds with T/P coupling whereas the underlying integrator cannot 
> conserve energy beyond a few tens of picoseconds. 
Have you tried LJ different from switch, e.g. cut-off?

> Many thanks, 
>   Istvan Kolossvary 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel

More information about the gromacs.org_gmx-users mailing list