On 06/17/2011 03:27 PM, ITHAYARAJA wrote:
Use a descriptive subject line.
On 17 June 2011 10:23, ITHAYARAJA <ithayar...@gmail.com <mailto:ithayar...@gmail.com>> wrote:Dear Sir, Above error was solved but the system has raised a following new error, i.e., Fatal error: 52 atoms are not part of any of the T-Coupling groups How do I find which atom file has problem? help me to solve this problem........... My position restraint parameter file is title = cpeptide position restraining warnings = 10 cpp = C:\Program Files\CTCBioapps\gromacs3.3\cpp.exe
Get an up-to-date version of GROMACS for much better performance.
define = -DPOSRES constraints = all-bonds integrator = md dt = 0.002 ; ps ! nsteps = 10000 ; total 20.0 ps. nstcomm = 1 nstxout = 250 ; output coordinates every 0.5 ps nstvout = 1000 : output velocities every 2.0 ps nstfout = 0 nstlog = 10 nstenergy = 10 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 rvdw = 1.0 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-5 optimize_fft = yes ; Berendsen temperature coupling is on in three groups Tcoupl = berendsen tau_t = 0.1 0.1 0.1 0.1 0.1 tc-grps = protein sol FAD NDP GSH ref_t = 300 300 300 300 300
Like I said before, go work out what is missing. How can we tell what atoms are missing? Also see the advice here http://www.gromacs.org/Documentation/Terminology/Thermostats
Mark
; Pressure coupling is not on Pcoupl = no pcoupltype = isotropic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 310.15 gen_seed = 173529/n -- Ithayaraja M, Research Scholar, Department of Bionformatics, Bharathiar University, Coimbatore 641 046, Tamil Nadu India
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