On 06/15/09, Bhanu <bhanui...@gmail.com> wrote: > > > > > On 15/06/2009, Mark Abraham <mark.abra...@anu.edu.au > <mark.abra...@anu.edu.au>> wrote: > > > > > > On 06/15/09, Bhanu <bhanui...@gmail.com <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 > > (http://oldwiki.gromacs.org/index.php/Errors#Range_Checking_error) > > > > Mark > > _______________________________________________ > > gmx-users mailing list gmx-us...@gromacs.org <gmx-users@gromacs.org> > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > (http://lists.gromacs.org/mailman/listinfo/gmx-users) > > Please search the archive at http://www.gromacs.org/search > > (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 > > <gmx-users-requ...@gromacs.org>. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > (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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