On Thu, Jun 30, 2011 at 7:57 PM, Jianguo Li <ljg...@yahoo.com.sg> wrote:
> Hi Amit, > > I also encountered the same problem you mentioned. > In v4.5, when using -nstlp wiht large value (e.g., 10000000), I got one > file "localpressure.dat0". I tested first several frames of a trajectory, > the calculated pressure is not the average of the pressure of individual > frames. > > In v4.5 it outputs the profile for frames in separate files which is ok. My concern is what exactly is going in v 4.0 where there is only one file for all the frames. Also where did you download v4.5 and v4.0 from ? > Btw, did you use CHARMM FF in your simulations and how did you convert the > tpr files from v 4.5 to v 4.0? > Yes i have used CHARMM FF and i will have to figure out the conversion. > > 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:* Friday, 1 July 2011 10:32:07 > *Subject:* Re: [gmx-users] Re: local pressure v4.5 issues > > 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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