remarks LANGTEST1 remarks This is a test file which builds a butane remarks molecule from 4 extended atoms and then runs remarks a series of Langevin dynamics tests. The initial remarks positions of the molecule are with the dihedral remarks angle at 180 degrees. Both bonds and bond angles remarks are SHAKen. rtf remarks rtf for butane MASS CH2E 14.02700 MASS CH3E 15.03500 RESIdue BUT ATOM C1 TYPE CH3E CHARGE 0.0 END ATOM C2 TYPE CH2E CHARGE 0.0 END ATOM C3 TYPE CH2E CHARGE 0.0 END ATOM C4 TYPE CH3E CHARGE 0.0 END BOND C1 C2 BOND C2 C3 BOND C3 C4 ANGLE C1 C2 C3 ANGLE C2 C3 C4 DIHEDRAL C1 C2 C3 C4 IC C1 C2 C3 C4 0.0 0.0 180.0 0.0 0.0 IC X C1 C2 C3 0.0 0.0 180.0 0.0 0.0 END {BUT} END !RTF parameter @TOPPAR:param11.pro end SEGMENT SETUPIC=T NAME=BUTE MOLECULE NAME=BUT NUMBER=1 END END IC FILL REFERENCE PARAMETERS END WRITE END BUILD SEED ( ATOM BUTE 1 C1 ) ( ATOM BUTE 1 C2 ) ( ATOM BUTE 1 C3 ) END END WRITE COOR END VECTOR DO ( FBETA = 6.657235 ) {1/ps} ( SEGID BUTE AND RESID 1 ) VECTOR SHOW ELEMENT ( FBETA ) ( ALL ) ! We SHAKE bonds and bond angles to simplify things SHAKE TOL=1.0E-5 BONDS (all) (all) ANGLES (all) (all) (all) END parameter NBONDS NBXMOD 4 END end energy end WRITE COOR END ! Run 2.5 ps of Langevin dynamics with initial temperature ! set to 291.0 K. Save the trajectory to analyze the rms ! fluctuations. set seed=71403814. end DYNA LANG TIMESTEP=0.001 NSTEP=2500 FIRSTT=290.0 FINALT=291.4 TWINDL=100.0 TWINDH=100.0 ILBFRQ=2500 IEQFRQ=0 IPRFRQ=0 NPRINT=20 iasvel=maxwell TBATH=291.0 trajectory=langtest1.dat NSAVC=5 END WRITE COOR END CLOSE langtest1.dat END DYNAMICS ANALYSIS AVERAGE input=langtest1.dat BEGIN=5 STOP=2500 SKIP=5 END vector show element ( b ) ( ALL ) close langtest1.dat end open langtest1.dat access=append end close langtest1.dat disp=delete end STOP