[gmx-users] mdrun -rerun

[Juliette N.]

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


>> 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.