[gmx-users] how long simulation takes to get stable when constrains is none in mdp file?

David van der Spoel spoel at xray.bmc.uu.se
Tue Aug 5 09:19:12 CEST 2008

wang kelvin wrote:
> hi:
> i am doing simulation of  a system consists of  512 DMSO moleculers and 
> 917 water moleculers.
> the whole system is running under 290K and 1bar ,and constraints = none;
> the simulation has taken 8000 ps ,but it seems not to get stable 
> yet,because RMSD keeps rising.
> when i did simulation of the same system with constraints set 
> all-bonds,it usually get stable within 3000ps.
> i wonder whether any mistakes has been made or it is normal.
> can you give some hints?
> thanks.

what rmsd?

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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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