On Wed, Sep 7, 2011 at 12:30 AM, Shou-Chuang Yang <shcy...@ucdavis.edu>wrote:
> > > On Wed, Sep 7, 2011 at 12:11 AM, Amit Choubey <kgp.a...@gmail.com> wrote: > >> >> >> On Tue, Sep 6, 2011 at 10:07 PM, Shou-Chuang Yang <shcy...@ucdavis.edu>wrote: >> >>> Dear gmx-users, >>> >>> Could anyone help me with the calculation of 3D pressure profile in a >>> function of y? >>> I used the provided gromacs-4.0.2_localpressure for my calculatioin. It >>> calculate >>> the 3D pressure profile as a function of z (the default setting of >>> bilayer normal >>> is z-direction). >>> >>> In my case, I have a bilayer which rotate at the first few nano second >>> run >>> and remained normal to y-directiona for the rest. How can I obtain a 3D >>> pressure analysis >>> along the y-direction? >>> >> Couldnt you rotate your box so that the bilayer is in z dir ? >> > > The local pressure analysis need to read the trajectory file with both > positions and velocities. > I thought of rotate my system and rerun it for the last 600 ns ( I am using > MARTINI), but since > I am also doing semiisotropic coupling, I cannot "rotate" the pressure > coupling directions. > > Another way I tried is to modify the output .trr into another .trr which y > and z columns printed out > reversely as well as the Vy and Vz columns. Thinking that maybe the > analysis code will read my > "originally y coordinates" as "z coordinates". What I got was segmentation > fault. > Why do you get a segmentation fault if you swap the y and z coordinates,velocity columns? Another way around is to change the simple_localpres_analysis.c code. If you look into it there is a loop that runs over boxes in z direction to calculate pressure tensor in z direction. You could change it to y. > I am not sure whether it will work out eventually. > >> I really appreciated your help! >>> >>> Thanks, >>> Joanne >>> -- >>> >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>> >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > > -- > Shou-Chuang Yang > Master’s Candidate > Department of Chemical Engineering and Materials Science > University of California, Davis > Phone: 1-646-639-4240 > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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