Hello Everyone, The git version of local pressure calculation at
http://repo.or.cz/w/gromacs.git/shortlog/refs/heads/release-4-5-localpressure is broken. I could not get it to work for my simulations. I installed gromacs local pressure version 4.0 from ftp://ftp.gromacs.org/pub/tmp/ I used gromacs-4.0.2_localpressure.tar.gz<ftp://ftp.gromacs.org/pub/tmp/gromacs-4.0.2_localpressure.tar.gz> in that folder. The pressure values printed using this version seem reasonable to me. I converted all the tpr files from v 4.5 to v 4.0. The output of the mdrun in v 4.0 is a single file "localpressure.dat" . On the contrary in v 4.5 there were separate "localpressure.dat*" files for each frame. I am not sure what exactly is the content of "localpressure.dat". Does it have the time averaged value of pressure tensor for each voxel ? It doesnt seem so to me because i tried it over only two frames (3 reruns were done for two frames separately and a .trr which had these two frames only) and the numbers did not seem to be averages. Can someone help me in figuring out what is going on ? Amit On Tue, Jun 21, 2011 at 9:16 AM, Amit Choubey <kgp.a...@gmail.com> wrote: > > > 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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