[gmx-users] Extracting enthalpies during or after MD
mark.abraham at anu.edu.au
Fri Jun 4 03:40:48 CEST 2010
----- 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
> 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.
> 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.
> > ----- 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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