Please make sure to keep the discussion on the mailing list.
On 9/1/15 9:35 AM, ANTHONY C MANSON wrote:
Thank You Justin: Can you tell me where in the code the actual energies for these groups are calculated.
See gmxlib/nonbonded/nonbonded.c, particularly do_nonbonded(); there are probably other locations in the code where bookkeeping and things are done but this is what seems to be accumulating all the pairwise interactions (I don't know the guts of this part of the code well).
I noted that some energy group calculations are done in nb_kernel_allvsall.c using a unit dielectric constant. This function is called indirectly by do_force_lowlevel(...) for each frame. I do not, however, think this is the correct code because the energies should be calculated every nstenergy frames.
nstenergy is for output being written to the .edr.
It is clear that these numbers seem high. I am trying to understand WHY they are so high. Is it the impact of the cutoff? especially in the Protein-SOL Coul-SR calculation. Can the cutoff be reduced say in a rerun type calculation ( I have reduced the cutoff in a rerun and the numbers scale down dramatically) -or- Are there still factors that cause the calculation to give large results? (such as not factoring in the dielectric constant of ~80 typically ascribed to water calculations)
Cutoffs are of course going to impact the magnitude of the value, as you've noticed, because shorter cutoffs simply mean fewer interactions are calculated in the short-range list. There is no need for dielectric values here; these are built into the parametrization of the water model (not all of them get the dielectric right). GROMACS allows for scaling of the vacuum dielectric (via epsilon_r), but this should not be altered for standard simulations as all force fields are parametrized using epsilon_r = 1 (you know, real physics :)
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 [email protected] | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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 [email protected].
