How large is the number? Does the large number converges? Lateral pressure is usually large (positive or negative) at the water-hydrophobic interface. e.g., see figures in this paper: J. Am. Chem. Soc. 2011, 133, 3720–3723.
Cheers, Jianguo ________________________________ From: Amit Choubey <kgp.a...@gmail.com> To: Jianguo Li <ljg...@yahoo.com.sg>; Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Wednesday, 22 June 2011 00:16:43 Subject: Re: [gmx-users] Re: local pressure v4.5 issues 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 >> >> >
-- 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
