Re: [gmx-users] Increase of 5-helix count
Hi, No single trajectory constitutes an experiment that should be expected to be replicable. You might have observed where the sun appeares to be at dawn today, but they observed where it was on November 7, 2014 and neither of those observations tells you anything about the range of positions the sun could actually appear to rise at, unless you have seen the sun rise for a couple of years. Mark On Wed, Jun 13, 2018, 08:25 Sundari wrote: > Kindly look at my query.. > > Thank you! > > On Mon, Jun 11, 2018 at 5:39 PM, Sundari wrote: > > > Dear gromacs users, > > > > I am running a simulation of three alpha helical peptides with a carbon > > nano tube in a simulation box. Actually I am following a paper and want > to > > reproduce the results. > > > > In my simulation every time there is a sudden increase of 5-helix count, > > means most of the alpha helix converted into 5-helix. > > > > I am using gromacs version 5.1.2. and paper used gromacs version 4. So I > > am confuse is this difference I am getting because of Gromacs version or > > something else? > > And 5-helix is not counted in total secondary structure count. > > (scount.xvg) > > please suggest something. > > > > > > Thank you in advance.. > > > > > > > > > > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Increase of 5-helix count
Kindly look at my query.. Thank you! On Mon, Jun 11, 2018 at 5:39 PM, Sundari wrote: > Dear gromacs users, > > I am running a simulation of three alpha helical peptides with a carbon > nano tube in a simulation box. Actually I am following a paper and want to > reproduce the results. > > In my simulation every time there is a sudden increase of 5-helix count, > means most of the alpha helix converted into 5-helix. > > I am using gromacs version 5.1.2. and paper used gromacs version 4. So I > am confuse is this difference I am getting because of Gromacs version or > something else? > And 5-helix is not counted in total secondary structure count. > (scount.xvg) > please suggest something. > > > Thank you in advance.. > > > > > > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Increase of 5-helix count
Dear gromacs users, I am running a simulation of three alpha helical peptides with a carbon nano tube in a simulation box. Actually I am following a paper and want to reproduce the results. In my simulation every time there is a sudden increase of 5-helix count, means most of the alpha helix converted into 5-helix. I am using gromacs version 5.1.2. and paper used gromacs version 4. So I am confuse is this difference I am getting because of Gromacs version or something else? And 5-helix is not counted in total secondary structure count. (scount.xvg) please suggest something. Thank you in advance.. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
