Dear all, I did another simulation with only SPC water. Then I used the local pressure gromacs to calculate the stresses. It seems to be reasonable.
I am not sure how to figure out what goes wrong with my previous simulations when plugged into the local pressure gromacs. Could someone help me in figuring out whats the issue ? Thank You. On Fri, Jun 17, 2011 at 6:00 PM, Amit Choubey <kgp.a...@gmail.com> wrote: > Dear all, > > I installed the git version of local pressure calculation from > > > http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure > > The I invoked mdrun > > mdrun_lp -v -s rerun.tpr -g rerun_log -olp -rerun traj0.gro -localpgrid 0.1 > > This created a file named "localpressure.dat0". This is a binary file so I > could not look at it directly. I am not sure if there is a tool in the > gromacs to look at it directly. > > To look at the data in "localpressure.dat0" I used the planar_av.c code > available in "pressure-tools" folder at > > http://md.chem.rug.nl/cgmartini/index.php/3d > > When I look at the Pressure tensor averaged over xy plane, some of the > numbers are reasonable but few of them are ridiculously large numbers which > is not expected. > > I checked this on two different simulations and I got the same problems. > The simulations had run OK previously. > > Could someone help me in figuring our whats going on ? > > Amit Choubey > >
-- 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
