[gmx-users] mdrun -rerun

[Justin A. Lemkul]

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

-- 
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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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