On Tue, Jun 21, 2011 at 1:13 AM, Jianguo Li <ljg...@yahoo.com.sg> wrote:
> Hi Amit, > > May I ask you a question? > In your calculation of local pressure using a trajectory file, did you get > a single averaged localpressure.dat file? Or else you get a bunch of > separate files for each frame (e.g., localpressure.dat0, localpressure.dat1, > localpressure.dat2 ....)? > Yes I do get different files for different trajectories. All the files seem to have the same problem ie a very large/small number printed as tensor elements of the pressure for some of the voxels. Do you have such problems ? Could we compare our methodologies to use the local pressure version ? Amit > > Thank you very much! > > Cheers, > Jianguo > > > ------------------------------ > *From:* Amit Choubey <kgp.a...@gmail.com> > *To:* Discussion list for GROMACS users <gmx-users@gromacs.org> > *Sent:* Monday, 20 June 2011 07:08:03 > *Subject:* [gmx-users] Re: local pressure v4.5 issues > > 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 >> >> >
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