Thanks for the addition. On 16 Feb 2018 6:22 pm, "Justin Lemkul" <jalem...@vt.edu> wrote:
> > > On 2/16/18 3:40 AM, Subhomoi Borkotoky wrote: > >> Hello, >> >> I believe *do_dssp* will do the trick. Generate the *.xpm* matrix file , >> it >> contains the required information. >> > > Only indirectly, but scount.xvg has all that is needed, the number of > residues in a given secondary structure as a function of time. From that, > percentage over time is a trivial scripting task, [(# in SS) / (# of > residues)]*100. > > -Justin > > Regards, >> >> S. Borkotoky >> >> On Fri, Feb 16, 2018 at 1:30 PM, Sundari <sundi6...@gmail.com> wrote: >> >> Dear gromacs users, >>> >>> can any one please tell me that how we get the secondary structure >>> propensity or secondary structure content(%) as a function of simulation >>> time. >>> >>> I used "gmx do_dssp" but it gives me number of residues forming the >>> secondary structure vs simulation time. is it same thing or something >>> different? >>> >>> 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. >>> >>> >> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > 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.