[gmx-users] Re: distance restraint

[Erik Marklund]

28 sep 2012 kl. 18.53 skrev pauladelgado:

> Yes i found this document "Computer simulations: Orientation of Lysozyme in
> vacuum under the influence of an electric field" where i found about the
> conditions i mentioned before for vacuum simulations. So what should i do?
> 

Find other literature. That document is a master thesis and not peer-reviewed material. I know the supervisor, and also the student to some extent, but even if I'd vouch for the methods used you should base your protocol primarily on peer-reviewed publications.

In my former group we published a few papers on protein simulations in vacuo (which were all NVE). See e.g.
Patriksson et al, Biochemistry 46:933-945 (2007)
Wang et al, Biochemistry 48:1006-1015 (2009)
Friemann et al, J. Am. Chem. Soc. 131:16606-+ (2009)
Marklund et al, PCCP 11:8069-8078 (2009)
Van der Spoel et al, Macromol. Biosci. 11:50-59 (2011)

Also have a look at the work of Modesto Orozco.

Best,

Erik

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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