Hello, Thanks for the response. But I have already done the trjconv pbc whole, nojump and center for my system to possibly fix this. Lemme try to check again from my orig trajectory file. Then I will get back to you. Thank you!
On Mon, Sep 17, 2018, 01:27 Justin Lemkul <jalem...@vt.edu> wrote: > > > On 9/16/18 12:16 PM, Stephani Macalino wrote: > > Hello, > > I ran a 100ns MD or a membrane protein and am now analyzing the APL and > > bilayer thickness from the trajectory file of 50,000 frames. > > When I graphed the values, around 20 to 30k frames in (and some frames > > along 40k) the value jumps from 40 to 70. The rest of the frames have > > pretty similar value at 40. > > Can you provide any idea why this happens? > > I already used trjconv in for my system before doing this. > > Have you visualized the trajectory to make sure all molecules were > imaged appropriately? It sounds to me like your lipids are simply > jumping across PBC. Sudden jumps or discontinuities in time series are > almost always due to PBC effects. > > -Justin > > -- > ================================================== > > 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.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.
