Re: namd: adding water molecules

From: Mgr. Lubos Vrbka (lubos.vrbka_at_uochb.cas.cz)
Date: Fri May 12 2006 - 00:51:02 CDT

hi,

> i had the rigidBonds set to all, so setting it to none it run without
> problems.
ok, it seems that the starting hydrogen positions were really 'wrong'
and the shake algorithm wasn't able to cope with them.

> i have two extra concerns:
> * how this setting will affect my simulation (compare to setting
> rigidBonds to all)
well, with rigidbonds, all the fastest vibrations (H vibrational
motions) are frozen - don't know how much difference this will make, but
one can never be sure. you should also probably decrease the timestep to
be sure that your integration algorithm will be stable. ...

> * i have to compare this simulation (with water inside the active site)
> vs others (without water, with substrate)that i already run. Do you
> think i'd run them again using rigidBonds none, or i can still compare
> them?
what about just minimizing your system without rigidbonds to relax the
hydrogen positions and then returning back to your normal simulation setup?

regards,
lubos

-- 
.....................................................
Mgr. Lubos Vrbka
Center for Biomolecules and Complex Molecular Systems
Institute of Organic Chemistry and Biochemistry
Academy of Sciences of the Czech Republic
Prague, Czech Republic
http://www.molecular.cz/~vrbka
.....................................................

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