Hi Yun-an Yan, In addition to the other things, COMM removal is also a source of energy drift. It is better to center your solute afterwards.
Cheers, Tsjerk On Thu, May 20, 2010 at 1:05 PM, Yan Yun-an <yun-an....@uni-rostock.de> wrote: > Dear Erik, > > Thank you so much for your prompt reply. I appreciate it. > > Yun-an Yan > > Erik Marklund writes: > >>For more exotic NVE-systems I had to do some or several of the following > >>things to get stable Etot: > >>* have an even shorter timestep than one would expect from the applied >>constraints and such. > > I will try a timestep with 0.5 fs. > >>* use double precision. > > The double precision is already in use. > >>* apply the constraints with lower tolerance/more iterations etc. > > I thought shake_tol = 1.e-8 is small enough. May I try an even smaller > value? > > Or the lincs algorithm with lincs_order=8 and lincs_iter=2 is recommended > > instead of shake? > >>Then there's a few things I notice in your setup: >>* I see that you do not use constrints at all. I would give it a shot. > > I will try. > >>* Why do you have two separate comm-grps? > > Since it is a solute-solvent fashion MD, I am trying to keeping the solute > > part close the center of the simulation box. But it does not work in this > way. > > Do you have any idea about that? > >>Erik Marklund >> >>-- >>----------------------------------------------- >>Erik Marklund, PhD student >>Dept. of Cell and Molecular Biology, Uppsala University. >>Husargatan 3, Box 596, 75124 Uppsala, Sweden >>phone: +46 18 471 4537 fax: +46 18 511 755 >>erikm at xray.bmc.uu.se http://folding.bmc.uu.se/ > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php