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.
