Re: [gmx-users] bilayer thickness 100ns membrane protein
Thnxx 4 your reply On Tue, Sep 18, 2018, 4:37 PM Stephani Macalino wrote: > 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? 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! > > > > > > > > *
Re: [gmx-users] bilayer thickness 100ns membrane protein
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? 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. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > >
Re: [gmx-users] bilayer thickness 100ns membrane protein
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 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? 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. > > > -- > 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.
Re: [gmx-users] bilayer thickness 100ns membrane protein
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? 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. > -- 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.
Re: [gmx-users] bilayer thickness 100ns membrane protein
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? 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.
Re: [gmx-users] bilayer thickness 100ns membrane protein
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? 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.
Re: [gmx-users] bilayer thickness 100ns membrane protein
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? 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.
Re: [gmx-users] bilayer thickness 100ns membrane protein
On 9/17/18 9:57 PM, Stephani Macalino wrote: 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? There is no one-size-fits-all or "required" set of trjconv commands. Visualize the output. If the molecules are properly re-imaged, you don't need to do anything else. -Justin Hope you can help. Thank you! Regards, Stephani On Mon, 17 Sep 2018 at 06:47, Stephani Macalino 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 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. -- == 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.
Re: [gmx-users] bilayer thickness 100ns membrane protein
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 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 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.
Re: [gmx-users] bilayer thickness 100ns membrane protein
Just to reinforce Justin's point, watch the trajectory. Especially around the time point at which you have seen the change in the values obtained. You can get a lot of information from just watching things, rather than looking at a number/graph that one of the analysis scripts spits out. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu - When the only tool you own is a hammer, every problem begins to resemble a nail. On Mon, 17 Sep 2018 at 08:11, Stephani Macalino 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 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. -- 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.
Re: [gmx-users] bilayer thickness 100ns membrane protein
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 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.
Re: [gmx-users] bilayer thickness 100ns membrane protein
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.
