Re: [gmx-users] Protein RMSD high
No, it's not at all significant in my problem as the loop is not part of the active site, way far at the two termini. I have plotted the RMSD in presence and absence of the loop. In absence of the loop rmsd is coming around 0.3 nm. Thanks Mark Tarak On Thu, Jun 27, 2013 at 2:37 PM, Mark Abraham wrote: > Your call. Is that motion significant to what you are trying to report > by your observation of the RMSD? > > Mark > > On Thu, Jun 27, 2013 at 9:03 AM, tarak karmakar > wrote: > > Dear All, > > > > While simulating a protein, I see the rmsd fluctuates around a mean of > 0.6 > > nm. I carefully looked at the trajectory (VMD movie) and saw there are > two > > flexible terminii fluctuating with a very high amplitude contributing to > > the high value of RMSD. Is it ok to report this problem with this RMSD > > value? > > > > Thanks > > Tarak > > -- > > gmx-users mailing listgmx-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 > -- > gmx-users mailing listgmx-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 > -- gmx-users mailing listgmx-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
Re: [gmx-users] Protein RMSD high
Your call. Is that motion significant to what you are trying to report by your observation of the RMSD? Mark On Thu, Jun 27, 2013 at 9:03 AM, tarak karmakar wrote: > Dear All, > > While simulating a protein, I see the rmsd fluctuates around a mean of 0.6 > nm. I carefully looked at the trajectory (VMD movie) and saw there are two > flexible terminii fluctuating with a very high amplitude contributing to > the high value of RMSD. Is it ok to report this problem with this RMSD > value? > > Thanks > Tarak > -- > gmx-users mailing listgmx-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 -- gmx-users mailing listgmx-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
[gmx-users] Protein RMSD high
Dear All, While simulating a protein, I see the rmsd fluctuates around a mean of 0.6 nm. I carefully looked at the trajectory (VMD movie) and saw there are two flexible terminii fluctuating with a very high amplitude contributing to the high value of RMSD. Is it ok to report this problem with this RMSD value? Thanks Tarak -- gmx-users mailing listgmx-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
