[gmx-users] Extracting enthalpies during or after MD

[lists at jsx.dk]

Aaah, I get it now (finally)... Thanks again...
Jesper


>
>
> ----- Original Message -----
> From: lists at jsx.dk
> Date: Saturday, June 5, 2010 5:58
> Subject: Re: [gmx-users] Extracting enthalpies during or after MD
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>
>> 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?
>
> Correct. The nonbonded loops tend to be (roughly) loops over energy groups
> over charge groups.
>
>> >> 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?
>
> No. Read manual 3.3 carefully - "mutual interactions between all energy
> monitor groups are compiled during the simulations". So you can get
> protein-lipid-head-group and protein-solvent (and the other pairs,
> including self-self, unless you use energy group exclusions) merely by
> defining three non-intersecting energy groups.
>
>> 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?
>
> Yes. g_enemat -h.
>
>> 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?
>
> You can do it with one invocation of mdrun, which is why I suggested that
> :-)
>
> Mark
>
>> >> 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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