[gmx-users] mdrun -rerun

Mark Abraham Mark.Abraham at anu.edu.au
Mon Apr 2 03:22:13 CEST 2012

On 2/04/2012 11:16 AM, 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.
>> 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?

Yes, per mdrun -h.

>>   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?

If you want new configurations based on some Frankenstein of your model 
physics, then you do not need mdrun -rerun.


> 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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