Dear Tsjerk, Do the virtual sites cause incorrect calculations of SASA, RMSD or something else?
Regards 2013/2/21 Tsjerk Wassenaar <tsje...@gmail.com> > Hi Ahmet, > > You can always use suitable index groups for analysis. > > Cheers, > > Tsjerk > > On Thu, Feb 21, 2013 at 7:08 AM, Ahmet yıldırım <ahmedo...@gmail.com> > wrote: > > I thought the virtual sites can affect analysis.For example, dont they > cause > > incorrect calculations of SASA, RMSD or something else? > > > > Thanks in advance > > > > 2013/2/20 Justin Lemkul <jalem...@vt.edu> > > > >> > >> > >> On 2/20/13 9:18 AM, Ahmet yıldırım wrote: > >> > >>> Dear users, > >>> > >>> I have the virtual sites in reference structure and all trajectory. > When > >>> analyzing simulation, do I have to get rid of those(virtual sites)? If > >>> yes/no, why? > >>> > >>> > >> Why do you think you need to remove them? > >> > >> -Justin > >> > >> -- > >> ==============================**========== > >> > >> Justin A. Lemkul, Ph.D. > >> Research Scientist > >> Department of Biochemistry > >> Virginia Tech > >> Blacksburg, VA > >> jalemkul[at]vt.edu | (540) 231-9080 > >> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin< > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > >> > >> ==============================**========== > >> -- > >> gmx-users mailing list gmx-users@gromacs.org > >> http://lists.gromacs.org/**mailman/listinfo/gmx-users< > http://lists.gromacs.org/mailman/listinfo/gmx-users> > >> * Please search the archive at http://www.gromacs.org/** > >> Support/Mailing_Lists/Search< > 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< > http://www.gromacs.org/Support/Mailing_Lists> > >> > > > > > > > > -- > > Ahmet Yıldırım > > -- > > 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 > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Biocomputing Group > Department of Biological Sciences > 2500 University Drive NW > Calgary, AB T2N 1N4 > Canada > -- > 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 > -- Ahmet Yıldırım -- 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
