Thanks Mark. I have several polymer chains (single polymer type) each having 362 atoms. So in order to exclude all nonbonded interactions of a chain with itself I need to add about 362 lines in the top file.
[exclusions] 1 2 3 ....362 2 3 4 ....362 3 4 5 ...362 . 358 .. 362 . . 360 361 362 (this is not needed even if I have nrexcl=3 in top file) - I guess I need only the above lines as in top file, [ molecules ] ; Compound #mols Polymer 10 takes care of the exclusions for all other existing chains? - Do I need to modify mdp file as well? energy_grps ? Thanks On 12 April 2012 20:58, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 13/04/2012 10:44 AM, Juliette N. wrote: >> >> Hello all, >> >> I am trying to exclude a nonbonded interactions on the polymer chains >> using >> >> grompp -f old.mdp -c old_em.gro -p nrexcl_new.top -o new.tpr >> >> and mdrun -rerun command. but when I issue the command above grompp >> takes many hours to finish and at the end grompp crashes (Killed). >> This even leads to some weired hardware problem which gibes failure of >> node having some CPUs..I mean when I get grompp failure, I am not able >> to connect to the node anymore and will have to restart the node! >> >> grompp gives: >> >> Generated 332520 of the 332520 1-4 parameter combinations >> Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp >> Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp >> Excluding 101 bonded neighbours molecule type 'Polymer' >> >> Can anyone help me please? > > > Justin explained the fundamental reason for the problem. Apparently the > implementation of the nrexcl=large is not robust with respect to memory > usage and/or CPU time for large numbers of exclusions. So you will have to > use energy group exclusions like I suggested earlier in this thread. > > Mark > > >> >> Thanks >> >> On 8 April 2012 17:16, Justin A. Lemkul<jalem...@vt.edu> wrote: >>> >>> >>> Juliette N. wrote: >>>> >>>> On 1 April 2012 20:17, Mark Abraham<mark.abra...@anu.edu.au> wrote: >>>>> >>>>> On 2/04/2012 10:10 AM, Juliette N. wrote: >>>>>> >>>>>> Hi all, >>>>>> >>>>>> I have an enquiry regarding calculation of heat of vaporization by >>>>>> estimating intermolecular nonbonded energies using mdrun rerun option. >>>>>> mdrun >>>>>> -rerun should break the total nonbonded energy coming from nonboded >>>>>> energy >>>>>> of (different molecules + a molecule with itself). By setting >>>>>> appropriate >>>>>> nrexcl in top file I am trying to exclude nonbonded part of molecule >>>>>> with >>>>>> itself within cut off radius so what remains would be intermolecular >>>>>> nonbonded energy between different molecules which determines heat of >>>>>> vaporization. >>>>>> >>>>>> 1) Is this approach correct? >>>>> >>>>> >>>>> For excluding a whole molecule, it could work. For excluding only a >>>>> part, >>>>> using energy group exclusions (see manual) is more flexible. Just >>>>> setting >>>>> energy groups suitably might work in your case, so that you get the >>>>> group-wise break-down of nonbonded energy. >>>>> >>>>> >>>>>> 2) If yes, can you please check the way I am applying mdrun rerun: >>>>>> >>>>>> grompp -p nrexcl_3.top -o total_nonbonded.tpr >>>> >>>> >>>> Hello all, >>>> >>>> I am a bit confused about whether or not mdp file has to be provided >>>> for grompp rerun step. In the original run (no mdrun I provide mdp as >>>> follows: >>>> >>>> grompp -f old.mdp -c old_em.gro -p nrexcl_3.top -o >>>> total_nonbonded.tpr (GROMPP old) >>>> then : >>>> mdrun -deffnm total_nonbonded -s -o -c -g -e >>>> >>>> Then I update the top file to new nrexcl= new value >>>> >>>> No do I have to provide the old mdp file and old gro file old_em.gro, >>>> which were used in (GROMPP old)? that is: >>>> >>>> (GROMPP new:) grompp -f old.mdp -c old_em.gro -p nrexcl_new.top >>>> -o new.tpr >>>> >>>> mpirun –np 4 mdrun_mpi -rerun total_nonbonded.trr –deffnm new -s -o >>>> -c -g -e -x >>>> >>>> >>>> >>>> or I just have to use: >>>> grompp -p nrexcl_new.top -o new.tpr ( no -c and no -f flag) >>>> >>> You need to provide some .mdp file and configuration. If you omit -c and >>> -f, grompp (like any other Gromacs program) will search for the default >>> names of grompp.mdp and conf.gro. If they don't exist, grompp will fail. >>> >>> >>>> My other question is that the grompp with large nrexcl around 100 is >>>> taking a lot of time, while the default nrexcl=3 was grompp ed much >>>> faster. Why excluding bonds in this way is time consuming? >>>> >>> It's going slower because it's doing exponentially more work. >>> >>> -Justin >>> >>> -- >>> ======================================== >>> >>> Justin A. Lemkul >>> Ph.D. Candidate >>> ICTAS Doctoral Scholar >>> MILES-IGERT Trainee >>> Department of Biochemistry >>> Virginia Tech >>> Blacksburg, VA >>> jalemkul[at]vt.edu | (540) 231-9080 >>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >>> >>> ======================================== >>> >>> -- >>> 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 >> >> >> > > -- > 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 -- Thanks, J. N. -- 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
