XPLOR-NIH version 2.9.5 C.D. Schwieters, J.J. Kuszewski, based on X-PLOR 3.851 by A.T. Brunger N. Tjandra, and G.M. Clore J. Magn. Res., 160, 66-74 (2003). http://nmr.cit.nih.gov/xplor-nih User: [unknown] on: x86/Linux at: 04-Jun-04 10:28:12 X-PLOR>remarks TIPSTEST1.INP X-PLOR>remarks This input file tests the minimum image periodic X-PLOR>remarks boundaries for TIP3P molecules. X-PLOR>remarks By Charles Brooks X-PLOR>remarks ================= X-PLOR> X-PLOR>rtf @TOPPAR:toph11.wat end ASSFIL: file /home/schwitrs/xplor/toppar/toph11.wat opened. RTFRDR>remarks TOPH11.WAT RTFRDR>remarks ========== RTFRDR>remarks topology file for water RTFRDR>remarks available: TIP3P model RTFRDR> RTFRDR>set echo=false end RTFRDR> end X-PLOR>parameter @TOPPAR:param11.wat end ASSFIL: file /home/schwitrs/xplor/toppar/param11.wat opened. PARRDR>remarks PARAM11.WAT (water parameters) PARRDR>remarks =========== PARRDR>remarks available: TIPS3P model PARRDR>set echo=false end PARRDR> end X-PLOR>! X-PLOR>! Set up a box of 125 water molecules X-PLOR>! X-PLOR>segment SEGMENT> name=wat SEGMENT> molecule MOLECULE> name=TIP3 number=125 MOLECULE> end SEGMENT>end SEGMNT: 125 residues were inserted into segment "WAT " XPLOR: current counts (number in parenthesis is maximum) NATOM= 375(MAXA= 400) NBOND= 250(MAXB= 400) NTHETA= 125(MAXT= 200) NGRP= 125(MAXGRP= 200) NPHI= 0(MAXP= 0) NIMPHI= 0(MAXIMP= 0) NDON= 0(MAXPAD= 0) NACC= 0(MAXPAD= 0) NNB= 0(MAXNB= 0) X-PLOR>coor COOR> REMARKS FILENAME="DISK$HUBER:[BRUNGER.CHARMM.CDT]TIPSTEST1.CHR;4" COOR> REMARKS This is a box of 125 water molecules in the experimental COOR> REMARKS geometry. The box was equilibrated previously by Monte Carlo COOR> REMARKS for the MCY potential. It is probably appropiate for starting COOR> REMARKS configurations for all 3-site water models. The box length COOR> REMARKS is 15.5516 A and the temperature and density are 300 K and COOR> REMARKS 0.0334 A**-3. COOR> REMARKS DATE: 4-FEB-84 11:09:36 created by user: BRUNGER COOR> NATOms = 375 COOR> 1 TIP3 OH2 -5.76008 3.27789 -3.46973 WAT 1 0.00000 X-PLOR> X-PLOR> X-PLOR>! X-PLOR>! X-PLOR>! Get the energy of this box without minimum image periodic boundaries X-PLOR>! Use the correct cutoff for TIP3P model. X-PLOR>! X-PLOR>{* right now the energy is computed in ENBOND as well as in ENTIPS *} X-PLOR> X-PLOR>parameter PARRDR> nbonds NBDSET> eps=1.0 cutnb=99.99 cdie truncation group NBDSET> end PARRDR>end X-PLOR>flags exclude angle bond end X-PLOR> X-PLOR>energy end MAKINB: mode 5 found 375 exclusions, 0 interactions(1-4) and 375 GB exclusions --------------- cycle= 1 -------------------------------------------------- | Etotal =-820.166 grad(E)=9.854 E(DIHE)=0.000 E(IMPR)=0.000 | | E(VDW )=78.235 E(ELEC)=-898.401 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>energy end --------------- cycle= 2 -------------------------------------------------- | Etotal =-820.166 grad(E)=9.854 E(DIHE)=0.000 E(IMPR)=0.000 | | E(VDW )=78.235 E(ELEC)=-898.401 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR> X-PLOR>! X-PLOR>! Now turn on minimum image convention X-PLOR>! Use the correct cutoff for TIP3P model. X-PLOR>! X-PLOR>xrefin XREFINE> a=15.5516 b=15.5516 c=15.5516 alpha=90. beta=90. gamma=90. XREFINE>end X-PLOR>flags FLAGS> include pvdw pele FLAGS>end X-PLOR>! X-PLOR>parameter PARRDR> nbonds NBDSET> cutnb=5.0 NBDSET> end PARRDR>end X-PLOR> X-PLOR>! X-PLOR>energy end MAKINB: mode 5 found 375 exclusions, 0 interactions(1-4) and 375 GB exclusions --------------- cycle= 3 -------------------------------------------------- | Etotal =-1087.972 grad(E)=11.435 E(DIHE)=0.000 E(IMPR)=0.000 | | E(VDW )=97.300 E(ELEC)=-872.882 E(PVDW)=24.883 E(PELE)=-337.272 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>parameter PARRDR> nbonds NBDSET> cutnb=7.5 NBDSET> end PARRDR>end X-PLOR>! X-PLOR>energy end MAKINB: mode 5 found 375 exclusions, 0 interactions(1-4) and 375 GB exclusions --------------- cycle= 4 -------------------------------------------------- | Etotal =-1178.345 grad(E)=12.142 E(DIHE)=0.000 E(IMPR)=0.000 | | E(VDW )=81.697 E(ELEC)=-773.786 E(PVDW)=9.093 E(PELE)=-495.349 | ------------------------------------------------------------------------------- X-PLOR>!!! this result doesn't quite match what a group-group minimum image X-PLOR>!!! calculation would produce. The reason lies in the fact that X-PLOR>!!! the list is generated with the group-group minimum image X-PLOR>!!! convention but the energies are then computed with an atom-atom X-PLOR>!!! minimum image convention. X-PLOR>! X-PLOR>stop HEAP: maximum use= 1001872 current use= 881017 X-PLOR: total CPU time= 0.2000 s X-PLOR: entry time at 10:28:12 04-Jun-04 X-PLOR: exit time at 10:28:12 04-Jun-04