Hello, I made sure that my protein is oriented in the z-axis using gmx editconf. My protein has extracellular domain. After orientation, you can check the structure if the EC domain is outside the membrane. If not, you can edit the Z-coordinate to move it along the z-axis. The topology file is automatically prepared by the charmm-gui. Regards, Stephani
On Tue, 18 Sep 2018 at 17:00, Bratin Kumar Das <177cy500.bra...@nitk.edu.in> wrote: > Dear stephani, > Did u modify anything in your initial protein > coordinate? Do u have any extracellular domain in your protein? How you > made the topology file after preparing the system in CHARMM-gui > > On Tue, Sep 18, 2018, 12:25 PM Stephani Macalino < > stephanimacal...@gmail.com> > wrote: > > > Hi Bratin, > > Sorry, I can't advise you on this. I am a newbie in this field as well. > > You might want to check charmm-gui for any contact information, and send > > them your question. > > In my experience, they reply quite fast. > > > > On Tue, 18 Sep 2018 at 15:34, Bratin Kumar Das < > > 177cy500.bra...@nitk.edu.in> > > wrote: > > > > > Dear Stephani, > > > I tried charmm-gui to pack the lipid bilayer > > > arround my protein. But charmm gui is giving fatal error. what possible > > > reason can be there for this fatal error. > > > > > > On Tue, Sep 18, 2018 at 11:01 AM, Stephani Macalino < > > > stephanimacal...@gmail.com> wrote: > > > > > > > Hello Bratin, > > > > I used charmm-gui to generate the MD input files and used CHARMM36 as > > > > forcefield. > > > > Then I used gromacs for the MD production run for 100ns. > > > > Once I got the trajectory files, I did the membrane analysis using a > > tcl > > > > script and gridmat. > > > > I followed the gromacs tutorial starting from the minimization. > > > > Regards, > > > > Stephani > > > > > > > > > > > > On Tue, 18 Sep 2018 at 14:25, Bratin Kumar Das < > > > > 177cy500.bra...@nitk.edu.in> > > > > wrote: > > > > > > > > > Dear Stephani, > > > > > Can u please tell me how you did the > > simulation > > > > and > > > > > what forcefield you used for your system. Did you followed the same > > > > > tutorial explained by justin lemkul > > > > > > > > > > On Sun, Sep 16, 2018 at 9:46 PM, Stephani Macalino < > > > > > stephanimacal...@gmail.com> 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. > > > > > > Should I run it for a longer time? > > > > > > Hope you can help. Thank you! > > > > > > Regards, > > > > > > Stephani > > > > > > -- > > > > > > 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? 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