Re: [gmx-users] Strange error in DNA simulations..
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. 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 listgmx-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
Re: [gmx-users] Strange error in DNA simulations..
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 listgmx-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 listgmx-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
Re: [gmx-users] Strange error in DNA simulations..
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 listgmx-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 listgmx-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 listgmx-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
