[gmx-users] mdrun -rerun

Juliette N. joojoojooon at gmail.com
Mon Apr 2 03:16:58 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.
>Thank you Mark. I have a one component system. I guess group exclusions is used for multicomponent systems where one needs to breakdown the total energies.? In my case I need to exclude non bonded interaction of a polymer chain with itself (avoid calculation of 1 and last atoms on chains if they fall within cutoff radius)
>> 2) If yes, can you please check the way I am applying mdrun rerun:
>> grompp -p nrexcl_3.top -o total_nonbonded.tpr
>> mdrun -deffnm total_nonbonded -s -o -c -g -e
>> I am done with these 5ns runs and now intend to exclude nonbonded
>> interaction on a chain by increasing nrexcl in top file named nrexcl_new.top
>> grompp -p nrexcl_new.top -o new.tpr
>> mdrun -rerun total_nonbonded.trr -s new.tpr -o new -c new -g new -e new
>> 2) Am I doing this correctly? I doubt because I provide -rerun
>> total_nonbonded.trr but dont know how to introduce -rerun
>> total_nonbonded.edr so that new energies get written on it?
> You want to write new energies and keep the old ones in case you need them.
> There's no reason to (want to) re-introduce the old ones. mdrun -rerun
> accepts the trajectory to determine what configurations to compute about. It
> doesn't need to know what some other algorithm thought about the energies of
> that configuration.
>I am a bit puzzled now. mdrun run takes on the old trajectory and recomputes energies based on the old trajectory for each frame? If thats the case, then use of nrexcel in order to obtain new trajectories fails I guess, as mdrun rerun does not produce a new trajectory but only a new energy file?!

In other words, say I am doing NPT, with default nrexcel =3 I got a
trajectory file and a density. Now with a new nrexcel that is large
enough to exclude all nonbonded interactions of atoms on the same
chain, I should expect a new trajectory and new density corresponding
to this modified nrexcel. My concern is if what mdrun reruns does is
just computing energies based on the old trajectory, I need to redo
the simulations with a new top file (nrexcel=new number) because this
new top file should affect the configuration. Am I right?

So for instance,
>> 3) If I want to re-calculate only the last 1 ns of runs (after system is
>> equilibrated), can I use -b 4000 ? i.e.:
>> mdrun -rerun total_nonbonded.trr -s new.tpr -o new -c new -g new -e new -b
>> 4000
> Probably not. Check mdrun -h, but either way you can use trjconv first.
> Mark
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J. N.

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