Hi, On Wed, Jun 15, 2016 at 12:05 PM Michael Brunsteiner < michael.brunstei...@tugraz.at> wrote:
> > Hi, > > In an attempt to understand how gromacs deals with electrostatic > (long range) interactions in systems with a net-charge i made couple > of simple model systems.... > Calculating the energy of a system with a SINGLE charge on only ONE atom > in a periodic system with PME I get: > > gmx energy -f one.edr > Coulomb (SR) -204.026 -- 0 0 (kJ/mol) > Coul. recip. 207.208 -- 0 0 (kJ/mol) > > (sys specs and input files below) > > Since I use PME i get as expected a non-zero "Coul. recip." while > Coulomb(SR)=-204.026 is the self energy (V_0 in eqn. 4.163 of the manual) > what i am missing is a correction term for systems with a net-charge > that is typically > proportional to the square of the net-charge divided by the volume. Is this > term included in Coul.recip Yes. See function ewald_charge_correction in the source code. > or do i have to calculate it myself and add > it explicitly? > > Is there a way to ask gromacs to explicitly provide: > 1) the individual terms in eqn. 4.161-4.163 of th3e manual > 2) the dipole correction (epsilon-surface>0) > 3) the net-charge correction > > ? > No, these are all dumped into Coul. recip. See code in src/gromacs/ewald/long-range-correction.cpp Mark > thanks for any help! > Michael > > > > ================================================== > system: > gromacs 5.1.2 on ubuntu 14.04, 64 bit > same result with both single and double prec. > > ================================================== > mdp file: > > integrator = md > nsteps = 0 > comm-grps = System > ; > nstxout = 0 > nstvout = 0 > nstfout = 0 > nstlog = 0 > nstenergy = 1 > ; > nstlist = 1 > ns_type = grid > pbc = xyz > rlist = 1.2 > cutoff-scheme = Verlet > ; > coulombtype = PME > rcoulomb = 1.2 > vdw_type = cut-off > rvdw = 1.2 > ; > constraints = none > continuation = yes > > ================================================== > top file: > > [ defaults ] > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ > 1 2 yes 0.5 0.8333 > > [ atomtypes ] > ;name bond_type mass charge ptype sigma epsilon > o o 10.00000 -1.00000 A 0.000000 0.000000 > c c 10.00000 1.00000 A 0.000000 0.000000 > n n 10.00000 0.00000 A 0.000000 0.000000 > > > [ moleculetype ] > ;name nrexcl > o 3 > > [ atoms ] > ; nr type resi res atom cgnr charge mass > 1 o 1 MM1 O 1 -1.00000 10.0000 > > > [ moleculetype ] > ;name nrexcl > c 3 > > [ atoms ] > ; nr type resi res atom cgnr charge mass > 1 c 1 MP1 C 1 1.00000 10.0000 > > > > [ moleculetype ] > ;name nrexcl > n 3 > > [ atoms ] > ; nr type resi res atom cgnr charge mass > 1 n 1 NEU N 1 0.00000 10.0000 > > > [ system ] > system > > [ molecules ] > n 1 > n 1 > n 1 > n 1 > n 1 > n 1 > n 1 > c 1 > > > ================================================== > input structure: > > CRYST1 41.461 66.148 200.000 90.00 90.00 90.00 P1 > ATOM 1 N NEU 1 20.000 30.000 100.000 0.00 0.00 > ATOM 2 N NEU 2 20.000 33.000 100.000 0.00 0.00 > ATOM 3 N NEU 3 23.000 33.000 100.000 0.00 0.00 > ATOM 4 N NEU 4 23.000 30.000 100.000 0.00 0.00 > ATOM 5 N NEU 5 20.000 30.000 103.000 0.00 0.00 > ATOM 6 N NEU 6 20.000 33.000 103.000 0.00 0.00 > ATOM 7 N NEU 7 23.000 33.000 103.000 0.00 0.00 > ATOM 8 C MP1 8 23.000 30.000 103.000 0.00 0.00 > > > > > > -- > ===================================================== > Michael Brunsteiner, PhD > Senior Researcher, Area II > Research Center Pharmaceutical Engineering GmbH > A-8010 Graz, Inffeldgasse 13 > phone: +43 316 873 30908 > mobile: +43 660 4887763 > fax: +43 316 873 109700 > e-mail: michael.brunstei...@rcpe.at > www.rcpe.at > UID-Nr.: ATU64272307 > FN: 312899x, FB-Gericht: LG für ZRS Graz > > Vertraulichkeitshinweis > Diese Nachricht und allfällige angehängte Dokumente sind vertraulich und > nur für den/die Adressaten bestimmt. > Sollten Sie nicht der beabsichtigte Adressat sein, ist jede Offenlegung, > Weiterleitung oder sonstige Verwendung > dieser Information nicht gestattet. In diesem Fall bitten wir, den > Absender zu verständigen und die Information zu > vernichten. Für Übermittlungsfehler oder sonstige Irrtümer bei > Übermittlung besteht keine Haftung. > > Confidentiality Note: > This message and any attached files are confidential and intended solely > for the addressee(s). Any publication, > transmission or other use of the information by a person or entity other > than the intended addressee is prohibited. > If you receive this in error please contact the sender and delete the > material. The sender does not accept liability > for any errors or omissions as a result of the transmission. > > -- > 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-requ...@gromacs.org. -- 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-requ...@gromacs.org.
