------------------------------------------------------- Amber 18 SANDER 2018 ------------------------------------------------------- | Run on 11/18/2018 at 16:06:08 | Executable path: /home/lnmiit/AMBER/amber18/bin/sander | Working directory: /home/karishma | Hostname: Unknown [-O]verwriting output File Assignments: | MDIN: polyAT_vac_md1_nocut.in | MDOUT: polyAT_vac_md1_nocut.out |INPCRD: polyAT_vac_init_min.rst | PARM: polyAT_vac.prmtop |RESTRT: polyAT_vac_md1_nocut.rst | REFC: refc | MDVEL: mdvel | MDFRC: mdfrc | MDEN: mden | MDCRD: polyAT_vac_md1_nocut.mdcrd |MDINFO: mdinfo | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj Here is the input file: 10-mer DNA MD in-vacuo, infinite cut off &cntrl imin = 0, ntb = 0, igb = 0, ntpr = 100, ntwx = 100, ntt = 3, gamma_ln = 1.0, tempi = 300.0, temp0 = 300.0 nstlim = 100000, dt = 0.001, cut = 999 / -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: | NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation |Largest sphere to fit in unit cell has radius = NaN ASSERTion ' n > 0 ' failed in ew_setup.F90 at line 306.