[gmx-users] RE: how long simulation takes to get stable when constrains is none in mdp file?
chaban at univer.kharkov.ua
Tue Aug 5 15:09:42 CEST 2008
>On Tue, Aug 5, 2008 at 9:19 AM, David van der Spoel
<spoel at xray.bmc.uu.se> wrote:
> wang kelvin wrote:
>> 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?
> what rmsd?
why it shouldn't rise? :)))
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
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