[gmx-users] mdrun -rerun

[Mark Abraham]

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.

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
>>>> --
>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>> Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>> interface
>>>> or send it to gmx-users-request at gromacs.org.
>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the www interface
>> or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>