[gmx-users] Re: DNA orientation restrain

Erik Marklund erikm at xray.bmc.uu.se
Mon Oct 8 11:29:23 CEST 2012


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.



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
> --
> View this message in context: http://gromacs.5086.n6.nabble.com/DNA-orientation-restrain-tp5001460p5001774.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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

More information about the gromacs.org_gmx-users mailing list