[gmx-users] A question on Berendsen NVT ensemble

David van der Spoel spoel at xray.bmc.uu.se
Tue Apr 30 22:39:32 CEST 2002

On Tue, 30 Apr 2002, Lianqing Zheng wrote:

>The material is still silica SiO2. Yes, I am trying to get liquid silica
>(then cool it down to get amorphous silica). So you are suggesting to use
>a smaller density at this temperature?
OK, let's assume your model is good enough, then I'd use editconf to
inflate the box (just scale by 2 in all directions). Then minimize the
enrgies to get the bonds OK, and finally run normal MD. If this is glassy
you probably need not go to 7000 K, but you know your material better than
I do. Take care to use short enough time steps. At room temp. you could
probably get away with say, 5 fs for SiO2. Since the velocity scales as
the scare root of the temperature you want to scale down the time step by
sqrt(7000/300) = 5, so 1 fs is borderline.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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