Hi! I have an issue with my protein modelling. I find that some of the helices (not all) have greatly unfolded during a 8ns distance restrained MD run. I am using the parameters below for the MD run. Is there any thing that can treat the system better than PME? thanks Jayant James
title = Yo cpp = /usr/bin/cpp define = -DDISRES constraints = none ;constraint_algorithm = lincs ;lincs_order = 4 integrator = md dt = 0.001 ; ps ! nsteps = 1000000 ; total 1.0ns. nstcomm = 1 nstxout = 5000 nstvout = 5000 nstfout = 5000 nstlog = 5000 nstenergy = 500 nstlist = 10 ns_type = grid rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.4 fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 4 ewald_rtol = 1e-5 optimize_fft = yes disre = simple disre_weighting = equal ; Berendsen temperature coupling is on in two groups Tcoupl = V-rescale tc-grps = tnc Non-Protein tnt NMR tni tau_t = 0.1 0.1 0.1 0.1 0.1 ref_t = 300 300 300 300 300 ; Energy monitoring energygrps = Protein Non-Protein ;tnc Non-Protein tnt NMR tni ; Pressure coupling is not on Pcoupl = parrinello-rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp = 300.0 gen_seed = 173529 -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp)
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