[gmx-users] Energy conservation with water

Eric Jakobsson jake at ncsa.uiuc.edu
Sun Feb 19 00:01:33 CET 2006

See Chiu, S.-W., Clark, M., Subramaniam, S., and E. Jakobsson. 2000. 
Collective motion artefacts arising in long-duration molecular 
dynamics simulations.   J. Comp. Chem. 21:121-131

At 09:09 PM 2/17/2006, you wrote:
>I'd suggest compiling in double precision, and running with the following
>dt                                   = 0.002
>nstlist                            = 10
>rlist                                = 1.2
>coulombtype               = PME
>rcoulomb                     = 1.1
>vdw-type                      = Switch
>rvdw                              = 1.1
>rvdw-switch                 = 1.05
>tcoupl                            = No
>pcoupl                          = No
>constraints                   = all-bonds
>constraint-algorithm   = shake
>unconstrained-start    = no
>Shake-SOR                 = no
>shake-tol                      = 1e-12
>This should give fairly good results for energy conservation.
>You may possibly need to used improved Ewald parameters; I had
>decent success with:
>fourierspacing           = 0.10
>pme_order                 = 6
>ewald_rtol                  = 1e-06
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Eric Jakobsson, Ph.D.
Professor, Department of Molecular and Integrative Physiology, and of 
Biochemistry, and of the Center for Biophysics and Computational Biology
Senior Research Scientist, National Center for Supercomputing Applications
Professor, Beckman Institute for Advanced Science and Technology
4021 Beckman Institute, mc251
University of Illinois, Urbana, IL 61801
ph. 217-244-2896       fax 217-244-2909

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