[gmx-users] LR electrostatics in single point energy calculations
jalemkul at vt.edu
Wed Jan 15 18:52:41 CET 2014
On 1/15/14, 11:57 AM, rajat desikan wrote:
> Hi Justin,
> I meant the pairwise interaction energies and not the total potential energy (I
> plan to define a 'interaction energy' by summing up all the individual terms). I
> followed your argument on the total potential energy of the protein being a
> function of the forcefield.
> I need the interaction parameters along with the LR terms. I am wondering how to
> do that.
> g_energy also gives me only the SR and 14 options. Here is part of a snapshot of
> the available options:
> 47 Box-Vel-ZZ 48 Coul-SR:Protein-Protein
> 49 LJ-SR:Protein-Protein 50 Coul-14:Protein-Protein
> 51 LJ-14:Protein-Protein 52 Coul-SR:Protein-POPC
> 53 LJ-SR:Protein-POPC 54 Coul-14:Protein-POPC
> 55 LJ-14:Protein-POPC 56 Coul-SR:Protein-SOL
There are no "LR" terms unless you use a twin-range cutoff scheme
(http://www.gromacs.org/Documentation/Gromacs_Utilities/g_energy). The PME mesh
term is written to the Coul-recip term. Decomposing it is not trivial.
> On Wed, Jan 15, 2014 at 10:17 PM, Justin Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
> On 1/15/14, 11:38 AM, rajat desikan wrote:
> Hi Justin,
> I used the following commands:
> mdrun_mpi -s md_6_50ns.tpr -rerun md_6_50ns.gro
> gmxdump_mpi -e ener.edr > ener_readme
> And in the dump of the ener_readme file, I have the following terms:
> Coul-SR:Protein-Protein -6.62324e+05
> LJ-SR:Protein-Protein -5.64854e+04
> Coul-14:Protein-Protein 4.04345e+05
> LJ-14:Protein-Protein 3.29438e+04
> Coul-SR:Protein-POPC -1.97403e+03
> LJ-SR:Protein-POPC -4.64531e+03
> Coul-14:Protein-POPC 0.00000e+00
> LJ-14:Protein-POPC 0.00000e+00
> There is neither a Coul-recip nor a Coul-LR term. So, I was wondering
> about it.
> The Coul-recip is the reciprocal space term in a Ewald summation
> right? I want the total potential energy of the protein. How would I go
> about that?
> I won't go into why "the total potential energy of the protein" is complete
> junk, because I explained all that last week.
> I don't know what to expect from gmxdump, but you should probably be using
> g_energy instead.
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.__edu
> <mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
> Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
Justin A. Lemkul, Ph.D.
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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