[gmx-users] Extracting enthalpies during or after MD

[lists at jsx.dk]

Thanks for the help Mark. Just to make sure I understand you correctly, I
have a few comments/questions, see below...

kind regards,
Jesper

> ----- Original Message -----
> From: lists at jsx.dk
> Date: Friday, June 4, 2010 10:35
> Subject: Re: [gmx-users] Extracting enthalpies during or after MD
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
>> Hi Mark,
>>
>> Thanks for the quick reply.
>>
>> The thing with the energy groups makes sense now. But I have run into
>> another problem with the method...
>>
>> The same atom cannot be in multiple energy groups during a simulation.
>
> It doesn't want to be... see manual 3.3

And there is no way to force it to be, right?

>
>> Let say that I want the interaction energy between water and lipid
>> head-group and also water and protein. Will I then have to do "mdrun
>> -rerun" to get all the energy group I want out of this?
>
> One (re)run will suffice unless you have large numbers of groups. Consider
> whether g_enemat is useful for you.


Using rerun will I be able to specify more energy groups, where the same
atom can be in multiple groups? Else, I would have to run it several
times, right?
Also, g_enemat is to post-process/analyse the numbers once I have them
from a simulation, where I have extracted all the energy numbers I want,
right?
So if I cannot do it with one simulations (because some atoms are part of
several different energy groups, then g_enemat won't work for my case,
correct?


>
>> And does mdrun -rerun work on a parallel cluster?
>
> Yes, it's exactly like mdrun, but derives the next positions from the
> trajectory, not from integration. If your groups are small, then use of
> energy group exclusions will make the problem small enough that you don't
> need parallelism, however.
>
> Obviously these interaction energies won't mean anything if you're using
> PME, since the long-range term can't be decomposed.
>
> Mark
>
>> > ----- Original Message -----
>> > From: lists at jsx.dk
>> > Date: Friday, June 4, 2010 8:47
>> > Subject: [gmx-users] Extracting enthalpies during or after MD
>> > To: gmx-users at gromacs.org
>> >
>> >> Hello,
>> >>
>> >> I am wondering if it is possible to output interaction
>> >> energies/enthalpiesduring an MD simulation between specific
>> >> groups of atoms.
>> >
>> > Yes. Look up "energy groups" in the manual.
>> >
>> >> The energies are all calculated anyways before the forces are
>> >> calculated,so I am wondering if there is an option to output
>> >> those energies to a
>> >> file?
>> >
>> > They'll go to the .edr file and be accessible with (e.g.) g_energy
>> >
>> >> I saw someone on the list who had re-coded gromacs to output these
>> >> energies, but this resulted in a significant slowdown of the
>> >> simulationbecause he made the code perform output in an inner-loop.
>> >
>> > Yep, don't do that.
>> >
>> >> If this is not an option, is there a clever way to get these
>> >> numbers out
>> >> after having run the simulation. Essentially, what I want is to
>> >> get the
>> >> enthalpy, between e.g. a PO4 head-group bead and a C1A tail-bead
>> >> using the
>> >> Martini FF.
>> >
>> > You can implement the above to happen during your simulation,
>> or use the
>> > facility of mdrun -rerun on a previously computed trajectory
>> with a
>> > suitable .tpr to recompute only the energies of the groups of
>> interest .
>> >
>> > Mark
>> >
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