[gmx-users] mdrun -rerun

[Juliette N.]

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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>>
>>
>>
>
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-- 
Thanks,
J. N.