[gmx-users] mdrun -rerun

[Juliette N.]

Hello all,

I am trying to exclude a nonbonded interactions on the polymer chains using

grompp -f old.mdp -c old_em.gro -p nrexcl_new.top -o new.tpr

and mdrun -rerun command. but when I issue the command above grompp
takes many hours to finish and at the end grompp crashes (Killed).
This even leads to some weired hardware problem which gibes failure of
node having some CPUs..I mean when I get grompp failure, I am not able
to connect to the node anymore and will have to restart the node!

grompp gives:

Generated 332520 of the 332520 1-4 parameter combinations
Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
Excluding 101 bonded neighbours molecule type 'Polymer'

Can anyone help me please?

Thanks

On 8 April 2012 17:16, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Juliette N. wrote:
>>
>> On 1 April 2012 20:17, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>>>
>>> On 2/04/2012 10:10 AM, Juliette N. wrote:
>>>>
>>>> Hi all,
>>>>
>>>> I have an enquiry regarding calculation of heat of vaporization by
>>>> estimating intermolecular nonbonded energies using mdrun rerun option.
>>>> mdrun
>>>> -rerun should break the total nonbonded energy coming from nonboded
>>>> energy
>>>> of (different molecules + a molecule with itself). By setting
>>>> appropriate
>>>> nrexcl in top file I am trying to exclude nonbonded part of molecule
>>>> with
>>>> itself within cut off radius so what remains would be intermolecular
>>>> nonbonded energy between different molecules which determines heat of
>>>> vaporization.
>>>>
>>>> 1) Is this approach correct?
>>>
>>>
>>> For excluding a whole molecule, it could work. For excluding only a part,
>>> using energy group exclusions (see manual) is more flexible. Just setting
>>> energy groups suitably might work in your case, so that you get the
>>> group-wise break-down of nonbonded energy.
>>>
>>>
>>>> 2) If yes, can you please check the way I am applying mdrun rerun:
>>>>
>>>> grompp -p nrexcl_3.top -o total_nonbonded.tpr
>>
>>
>> Hello all,
>>
>> I am a bit confused about whether or not mdp file has to be provided
>> for grompp rerun step. In the original run (no mdrun I provide mdp as
>> follows:
>>
>>            grompp -f old.mdp -c  old_em.gro -p nrexcl_3.top -o
>> total_nonbonded.tpr             (GROMPP old)
>> then :
>>            mdrun -deffnm total_nonbonded -s -o -c -g -e
>>
>> Then I update the top file to new nrexcl= new value
>>
>> No do I have to provide the old mdp file and old gro file old_em.gro,
>> which were used in  (GROMPP old)? that is:
>>
>>  (GROMPP new:)       grompp -f old.mdp -c old_em.gro -p nrexcl_new.top
>> -o new.tpr
>>
>> mpirun –np 4 mdrun_mpi -rerun total_nonbonded.trr  –deffnm new -s -o
>> -c -g -e -x
>>
>>
>>
>> or I just have to use:
>>  grompp   -p nrexcl_new.top -o new.tpr     ( no -c and no -f flag)
>>
>
> You need to provide some .mdp file and configuration.  If you omit -c and
> -f, grompp (like any other Gromacs program) will search for the default
> names of grompp.mdp and conf.gro.  If they don't exist, grompp will fail.
>
>
>>
>> My other question is that the grompp with large nrexcl around 100 is
>> taking a lot of time, while the default  nrexcl=3 was grompp ed much
>> faster. Why excluding bonds in this way is time consuming?
>>
>
> It's going slower because it's doing exponentially more work.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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-- 
Thanks,
J. N.