------------------------------------------------------- Amber 22 SANDER 2022 ------------------------------------------------------- | Run on 03/22/2023 at 21:12:28 | Executable path: sander.MPI | Working directory: /home/munazzah/Remd/Test_for_restart/Remd_imp_droso | Hostname: phoenix [-O]verwriting output File Assignments: | MDIN: /home/munazzah/Remd/Test_for_restart/Remd_imp_droso/5.Production/remd1 | MDOUT: /home/munazzah/Remd/Test_for_restart/Remd_imp_droso/5.Production/remd. |INPCRD: /home/munazzah/Remd/Test_for_restart/Remd_imp_droso/5.Production/remd. | PARM: /home/munazzah/Remd/Test_for_restart/Remd_imp_droso/2.Solvation/1urr.p |RESTRT: /home/munazzah/Remd/Test_for_restart/Remd_imp_droso/5.Production/remd. | REFC: refc | MDVEL: mdvel.000 | MDFRC: mdfrc.000 | MDEN: mden.000 | MDCRD: /home/munazzah/Remd/Test_for_restart/Remd_imp_droso/5.Production/remd. |MDINFO: /home/munazzah/Remd/Test_for_restart/Remd_imp_droso/5.Production/remd. | MTMD: mtmd |INPDIP: inpdip |RSTDIP: rstdip |INPTRA: inptraj | REMLOG: /home/munazzah/Remd/Test_for_restart/Remd_imp_droso/5.Production/rem.log | REMTYPE: rem.type | REMSTRIP: | SAVEENE: saveene |CLUSTERINF: cluster.info | RESERVOIR: reserv/frame | REMDDIM: Here is the input file: &cntrl imin = 0, irest = 1, ntx = 5, ntt = 3, gamma_ln = 2.0, temp0 = 300.00, ig = -1, ntc = 2, ntf = 2, ntb = 0, igb = 5, cut = 999.0, rgbmax = 999.0, ntpr = 5000, ntwx = 5000, ntwr = 5000, nmropt = 1, nscm = 500, numexchg = 1000, nstlim = 50000, dt = 0.002, &end / &wt TYPE='END' / DISANG=/home/munazzah/Remd/Test_for_restart/Remd_imp_droso/5.Production/1u -------------------------------------------------------------------------------- 1. RESOURCE USE: -------------------------------------------------------------------------------- | Flags: MPI | New format PARM file being parsed. | Version = 1.000 Date = 12/26/22 Time = 18:25:27 NATOM = 1588 NTYPES = 14 NBONH = 789 MBONA = 817 NTHETH = 1796 MTHETA = 1095 NPHIH = 3610 MPHIA = 3420 NHPARM = 0 NPARM = 0 NNB = 8726 NRES = 97 NBONA = 817 NTHETA = 1095 NPHIA = 3420 NUMBND = 65 NUMANG = 152 NPTRA = 192 NATYP = 33 NPHB = 0 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0 NCOPY = 0 Implicit solvent radii are H(N)-modified Bondi radii (mbondi2) | Memory Use Allocated | Real 632182 | Hollerith 4863 | Integer 119962 | Max Pairs 1 | nblistReal 0 | nblist Int 0 | Total 5426 kbytes | Note: 1-4 EEL scale factors are being read from the topology file. | Note: 1-4 VDW scale factors are being read from the topology file. | Duplicated 0 dihedrals | Duplicated 0 dihedrals Note: ig = -1. Setting random seed to 792703 based on wallclock time in microseconds and disabling the synchronization of random numbers between tasks to improve performance. -------------------------------------------------------------------------------- 2. CONTROL DATA FOR THE RUN -------------------------------------------------------------------------------- default_name General flags: imin = 0, nmropt = 1 Replica exchange numexchg= 1000, rem= 1 Nature and format of input: ntx = 5, irest = 1, ntrx = 1 Nature and format of output: ntxo = 2, ntpr = 5000, ntrx = 1, ntwr = 5000 iwrap = 0, ntwx = 5000, ntwv = 0, ntwe = 0 ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat= 0 Potential function: ntf = 2, ntb = 0, igb = 5, nsnb = 25 ipol = 0, gbsa = 0, iesp = 0 dielc = 1.00000, cut = 999.00000, intdiel = 1.00000 saltcon = 0.00000, offset = 0.09000, gbalpha= 1.00000 gbbeta = 0.80000, gbgamma = 4.85000, surften = 0.00500 rdt = 0.00000, rgbmax = 999.00000 extdiel = 78.50000 alpb = 0 Frozen or restrained atoms: ibelly = 0, ntr = 0 Molecular dynamics: nstlim = 50000, nscm = 500, nrespa = 1 t = 0.00000, dt = 0.00200, vlimit = 20.00000 Langevin dynamics temperature regulation: ig = 792703 temp0 = 300.00000, tempi = 0.00000, gamma_ln= 2.00000 SHAKE: ntc = 2, jfastw = 0 tol = 0.00001 NMR refinement options: iscale = 0, noeskp = 1, ipnlty = 1, mxsub = 1 scalm = 100.00000, pencut = 0.10000, tausw = 0.10000 | MPI Timing options: | profile_mpi = 0 | INFO: Old style inpcrd file read -------------------------------------------------------------------------------- 3. ATOMIC COORDINATES AND VELOCITIES -------------------------------------------------------------------------------- | Overwriting temp0 from mdin with temp0 from netcdf inpcrd file default_name begin time read from input coords =272650.000 ps Begin reading energy term weight changes/NMR restraints WEIGHT CHANGES: ** No weight changes given ** RESTRAINTS: Requested file redirections: DISANG = /home/munazzah/Remd/Test_for_restart/Remd_imp_droso/5.Production/1u Restraints will be read from file: /home/munazzah/Remd/Test_for_restart/Remd_imp_droso/5.Production/1u Here are comments from the DISANG input file: # # chirality for residue 1 atoms: CA CG1 CG2 HB Number of restraints read = 347 Done reading weight changes/NMR restraints Number of triangulated 3-point waters found: 0 | Atom division among processors: | 0 1588 | Running AMBER/MPI version on 1 nodes | MULTISANDER: 12 groups. 1 processors out of 12 total.