On Wed, Sep 7, 2011 at 12:11 AM, Amit Choubey <[email protected]> wrote:
> > > On Tue, Sep 6, 2011 at 10:07 PM, Shou-Chuang Yang <[email protected]>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. I am not sure whether it will work out eventually. > I really appreciated your help! >> >> Thanks, >> Joanne >> -- >> >> >> -- >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > 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
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