[gmx-users] Re: DNA orientation restrain

[Erik Marklund]

Hi,

Yes. Although not applicable to all systems, as you correctly state, a slightly extended periodic DNA helix could still yield a smaller box since the non-periodic molecule would need a minimum distance to its periodic copy, the length of which depending on the non-bonded interactions. Hence, extending the helix by a few nucleotides could be worth it, depending on what you aim to study. On the other hand, neighbor searching is a bit slower when there are periodic molecules are present in the system, but I do not know how much of an effect that has on performance.

Best,

Erik

8 okt 2012 kl. 10.01 skrev Tong Dudu:

> Thanks, Erik.
> 
> Actually, I tried to use periodic molecules in my previous simulations. But
> I think that can be only applied to DNA molecules of certain length, say
> 10bps, 20bps. But my DNA molecule here doesn't meet that criteria.
> 
> Dudu
> 
> 
> 
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html