[gmx-users] mdrun -rerun

[Juliette N.]

Thanks Mark. I have several polymer chains (single polymer type) each
having 362 atoms. So in order to exclude all nonbonded interactions of
a chain with itself I need to add about 362 lines in the top file.

[exclusions]
1 2 3 ....362
2 3 4 ....362
3 4 5 ...362
.
358 .. 362
.
.
360 361 362 (this is not needed even if I have nrexcl=3 in top file)

- I guess I need only the above lines as in top file,

[ molecules ]
; Compound        #mols
Polymer             10

takes care of the exclusions for all other existing chains?

- Do I need to modify mdp file as well? energy_grps ?

Thanks

On 12 April 2012 20:58, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 13/04/2012 10:44 AM, Juliette N. wrote:
>>
>> 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?
>
>
> Justin explained the fundamental reason for the problem. Apparently the
> implementation of the nrexcl=large is not robust with respect to memory
> usage and/or CPU time for large numbers of exclusions. So you will have to
> use energy group exclusions like I suggested earlier in this thread.
>
> Mark
>
>
>>
>> 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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>>
>>
>>
>
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-- 
Thanks,
J. N.