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! 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.
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