Hi all! I am quite new to Gromacs and am wondering why I can´t see any box fluctuations during a NPT run of protein + urea solvent in dodecahedron. In the energy output file I can see that the Box-X,Y,Z values only fluctuate <1%.
However the pressure average is reasonably close to the ref_p value, 1.7 instead of 1.0 during 20ns. Should there not be any box fluctuations with the parrinello-rahman algorithm? I use the input settings specified below. title = Dyna cpp = /usr/bin/cpp constraints = hbonds constraint_algorithm = lincs lincs_iter = 1 integrator = md dt = 0.002 nsteps = 8000000 nstxout = 4000000 nstvout = 3000 nstlog = 250 nstenergy = 250 nstxtcout = 250 xtc_grps = energygrps = Protein SOL UREA CL- nstlist = 5 ns_type = grid rlist = 1.1 coulombtype = PME rcoulomb = 1.1 rvdw = 1.4 fourierspacing = 0.14 pme_order = 6 optimize_fft = yes tcoupl = nose-hoover tc-grps = Protein SOL UREA CL- tau_t = 0.5 0.5 0.5 0.0 ref_t = 308 308 308 308 Pcoupl = parrinello-rahman tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 Thank you! Regards Matteus Lindgren Graduate student Department of Chemistry Umeå University SE-901 87 Umeå, Sweden Tel: +46 (0)90 786 53 68 e-mail: <mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED]
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