[gmx-users] mdrun -rerun

Juliette N. joojoojooon at gmail.com
Sun Apr 8 23:13:08 CEST 2012

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

            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)

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?

Appreciate your comments,

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