[gmx-users] LR electrostatics in single point energy calculations
rajatdesikan at gmail.com
Wed Jan 15 17:38:44 CET 2014
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:
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
calculation, right? I want the total potential energy of the protein. How
would I go about that?
On Wed, Jan 15, 2014 at 7:39 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 1/15/14, 7:14 AM, rajat desikan wrote:
>> Hi All,
>> I was wondering about the long range electrostatics while calculating
>> single point energies. I did a cursory calculation for a protein in water
>> (PME) and found that the LR electrostatic terms were zero. I know that the
>> per-particle decomposition of the LR electrostatics is non trivial. I was
>> wondering if there is a way to do it in Gromacs?
> Was the Coul-recip term actually zero, or were you looking at Coul-LR?
> The two terms mean very different things.
> 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 | (410) 706-7441
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
More information about the gromacs.org_gmx-users