Hello again, I have pinpointed the problem I have. I tried to follow http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow . But I only used pbc whole, nojump and mol center. After I used nojump, the thickness values of my trajectory is stable at around 40. After I use -pbc mol - center, the strange value jumps are observed. I want to know if it is okay to just leave off the mol center? Hope you can help. Thank you! Regards, Stephani
On Mon, 17 Sep 2018 at 06:47, Stephani Macalino <stephanimacal...@gmail.com> wrote: > 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.