[gmx-users] mdrun -rerun in parallel?

[Mark Abraham]

On 2/04/2012 1:57 PM, Juliette N. wrote:
> Hi all,
>
> Is there anyway mdrun -rerun can be used on multiple nodes? e.g. -nt?

Yes. You could have just tried it :-) It's just a version of mdrun that 
gets configurations from the magic file, doesn't actually do integration 
steps and does neighbour searching every configuration.

Mark

>
> Best,
>
>
> ---------- Forwarded message ----------
> From: Juliette N.<joojoojooon at gmail.com>
> Date: 1 April 2012 22:10
> Subject: Re: [gmx-users] mdrun -rerun
> To: Discussion list for GROMACS users<gmx-users at gromacs.org>
>
>
> On 1 April 2012 22:07, Mark Abraham<Mark.Abraham at anu.edu.au>  wrote:
>> On 2/04/2012 12:05 PM, Juliette N. wrote:
>>> Thanks. One last question. So whats the new trr file provided by -o
>>> flag of mdrun rerun below?
>>>
>>> mdrun -rerun total_nonbonded.trr -s new.tpr -o new -c new -g new -e new
>>
>> If it even writes one, it will be identical to the -rerun file. There's no
>> way for the rerun code to get new configurations except by reading the input
>> trajectory.
> Thanks a lot :)
>> Mark
>>
>>
>>>>> 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.
>>>>
>>>> Mark
>>>>
>>>>
>>>>> 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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>>>>>
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>
>
> --
> Thanks,
> J. N.
>
>