I have tried CHARMM FF in v4.0.4 and it does not give error, so it seems dihedral type 9 has already been implemented in v4.0.4. Jianguo
________________________________ From: Jianguo Li <ljg...@yahoo.com.sg> To: Amit Choubey <kgp.a...@gmail.com> Cc: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Thursday, 28 July 2011 15:05:19 Subject: Re: [gmx-users] Re: local pressure v4.5 issues Use grompp of v4.0.7 to generate the tpr files using CHARMM FF and give this tpr file to v4.0.2_local_pressure to rerun the simulation. 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: Thursday, 28 July 2011 09:27:04 Subject: Re: [gmx-users] Re: local pressure v4.5 issues 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 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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