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 That document is a master thesis and not peer-reviewed material.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 > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/distance-restraint-tp5001387p5001411.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > gmx-users mailing list gmx-users@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-requ...@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 er...@xray.bmc.uu.se http://www2.icm.uu.se/molbio/elflab/index.html -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
