Hi all, I am trying to figure out a way to port tpr files (which has CHARMM FF) from v4.5 to v4.0.2. This is because i want to use the localpressure calculation which works only in version 4.0.2.
When i issue the following command i get grompp_v4.0.2_lp -v -c traj0.gro -o npt_4.0 -p system.top -f rerun.mdp I get the following error * * Program grompp_v4.0.2_lp, VERSION 4.0.2_localpressure Source code file: topdirs.c, line: 118 Fatal error: Invalid dihedral type 9 I think dihedral type 9 is not defined until version 4.0.7. Could anyone provide a way to deal with this ? Amit On Thu, Jun 30, 2011 at 9:39 PM, Jianguo Li <ljg...@yahoo.com.sg> wrote: > I downloaded v4.5 and v4.0 from the same websites as you mentioned in > previous email. I am not sure why v4.5 give inconsistent results. I haven't > try v4.0, because my simulation is using CHARMM FF. Could you give more > details of conversion tpr files from v4.5 to v4.0 using CHARMM FF? > > Thank you very much! > > Cheers, > Jianguo > > > > ------------------------------ > *From:* Amit Choubey <kgp.a...@gmail.com> > *To:* Jianguo Li <ljg...@yahoo.com.sg> > *Cc:* Discussion list for GROMACS users <gmx-users@gromacs.org> > *Sent:* Friday, 1 July 2011 11:47:58 > > *Subject:* Re: [gmx-users] Re: local pressure v4.5 issues > > > > 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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