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

[Tsjerk Wassenaar]

why RMSD?

On Tue, Aug 5, 2008 at 9:19 AM, David van der Spoel
<spoel at xray.bmc.uu.se> wrote:
> 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.
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623