[gmx-users] Strange error in DNA simulations..

[Bhanu]

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.abraham at anu.edu.au> wrote:
>
>
>
> On 06/15/09, *Bhanu *<bhanuiitr at gmail.com> wrote:
>
>
>
> On 15/06/2009, Mark Abraham <mark.abraham at anu.edu.au> wrote:
>>
>>
>> On 06/15/09, *Bhanu *<bhanuiitr at 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 at 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-request at 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 at 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-request at 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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090615/07cb3543/attachment.html>