You can see the radius of gyration, number of hydrogen bond, native contact etc for assessing the stability
On Sun 15 Sep, 2019, 4:32 PM Quin K, <profiles...@gmail.com> wrote: > Thank you! > What else should I be looking for? > [image: mailcastr branding] Sent with Mailcastr > < > https://mailcastr.com/?utm_source=chrome-extension&utm_medium=branded-email&utm_campaign=BRANDING > > > > On Sun, Sep 15, 2019 at 4:16 PM Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 9/15/19 5:30 AM, Quin K wrote: > > > Hi everyone! > > > > > > I have done a MD simulation for a protein structure at 310K (100ns) > this > > is > > > the RMSD at around 65 ns kindly comment on the stability. Will I have > to > > > rerun the MD? > > > Kindly let me know how to decide stability by analyzing RMSD. > > > > RMSD alone is generally insufficient to make any definitive conclusions > > about stability. I see nothing out of the ordinary in the plot. > > > > -Justin > > > > > For backbone > > > < > > > https://drive.google.com/file/d/18JjiAKivbWklIXRSVaqhQ2zMUN9L_hkl/view?usp=sharing > > > > > > For backbone xvg file > > > < > > > https://drive.google.com/file/d/12MBTO57f_xROW5mWTFtMskwTNL1gCvam/view?usp=sharing > > > > > > For protein > > > < > https://drive.google.com/file/d/1LrdIFxQ-rBrIkcgbnfgEHg424cKgGm7_/view> > > > For protein - expanded > > > < > https://drive.google.com/file/d/1yvwLzdYMAenL9n1kOdaVzOo5JU6j4YU-/view> > > > For protein xvg file > > > < > > > https://drive.google.com/file/d/1hKbbTOCLqG7xDySQ7r4VcrNfSaokmYJO/view?usp=sharing > > > > > > > > > > > > Thank you in advance. > > > > > > Regards! > > > > > > < > > > http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail > > > > > > Virus-free. > > > www.avg.com > > > < > > > http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail > > > > > > <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > > > > -- > > ================================================== > > > > Justin A. Lemkul, Ph.D. > > Assistant Professor > > Office: 301 Fralin Hall > > Lab: 303 Engel Hall > > > > Virginia Tech Department of Biochemistry > > 340 West Campus Dr. > > Blacksburg, VA 24061 > > > > jalem...@vt.edu | (540) 231-3129 > > http://www.thelemkullab.com > > > > ================================================== > > > > -- > > 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. > -- 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.