Hi, I didn't ignore your link, I was trying all things suggested in wiki.. Its the greed for more and more suggestions made me to type those..
Anyway, thanks for the link, buddy! On 15/06/2009, Mark Abraham <mark.abra...@anu.edu.au> wrote: > > > > On 06/15/09, *Bhanu *<bhanui...@gmail.com> wrote: > > > > On 15/06/2009, Mark Abraham <mark.abra...@anu.edu.au> wrote: >> >> >> On 06/15/09, *Bhanu *<bhanui...@gmail.com> wrote: >> >> Hi Group, >> I've tried simulating a five bp dna. It has showed many atoms missing and >> some extra atoms present in the pdb file. For pdb2gmx, I used -ignh and >> -mising options. Later editconf_d, genbox_d, and genion_d steps went well. >> Even grompp_d worked well. But when I issued the run command for mdrun_d, >> the strange result is coming, repeatedly. I have installed lam-mpi and >> running gromacs in double precision. The commands I have used are.. >> >> pdb2gmx_d -f fivedna.pdb -o dna.gro -p dna.top >> editconf_d -f dna.gro -bt dodecahedron -c -d 1.0 -o boxdna.gro >> genbox_d -cp boxdna.gro -cs spc216.gro -p dna.top -o solvateddna.gro >> >> neutralized the system with genion_d and grompp_d, mdrun_d with -v and >> -deffnm commands. Surprisigly, everytime, it is using only two cores of my >> core2quad processor, delaying the output for all experiments. >> >> So look up how to configure LAM-MPI to use more. >> > > > I am working on that.. but the real confusing thing, is why are DNA > simulations failing?? I have no clue.. and requesting for a suggestion! > > I gave you a link to content that was likely to explain why your problem > was occurring. If you appear to ignore it, then you won't be likely to get > more :-) > > Mark > > > > >> For this experiment, here is the error report which I donot understand >> at all! >> >> The error report is really frightening to me!!! Here it is! >> >> >> See http://oldwiki.gromacs.org/index.php/Errors#Range_Checking_error >> >> Mark >> >> _______________________________________________ >> 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/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/mailing_lists/users.php >> > > > > -- > Never lose hope on the person you love.... they maybe the reason your heart > aches today... but they are definitely the reason your heart beats.... : > COPIED FROM GMAIL CUSTOM MSGS. > > > _______________________________________________ > 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/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/mailing_lists/users.php > -- Never lose hope on the person you love.... they maybe the reason your heart aches today... but they are definitely the reason your heart beats.... : COPIED FROM GMAIL CUSTOM MSGS.
_______________________________________________ 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/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/mailing_lists/users.php