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<div>Dear all,</div>
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<div>I am working on a biological dimer of 330 residues.</div>
<div>I dont think that I got any error message when I did grompp.</div>
<div>Please find pr.mdp filesbelow and RMSD as attachment.</div>
<div>Please tell me why it happened?</div>
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<div>pr.mdp </div>
<div>;<br>; User spoel (236)<br>; Wed Nov 3 17:12:44 1993<br>; Input file<br>title = CM_2ao2_A<br>cpp = /usr/bin/cpp<br>define = -DPOSRES<br>constraints = all-bonds<br>
integrator = md<br>dt = 0.001<br>nsteps = 100000<br>nstcomm = 1<br>nstxout = 250<br>nstvout = 1000<br>nstfout = 0<br>nstlog = 10<br>
nstlist = 10<br>ns_type = grid<br>rlist = 1<br>coulombtype = PME<br>rcoulomb = 1.0<br>rvdw = 1.0<br>fourierspacing = 0.12<br>fourier_nx = 0<br>
fourier_ny = 0<br>fourier_nz = 0<br>pme_order = 4<br>ewald_rtol = 1e-5<br>optimize_fft = yes<br>;<br>; Berendsen temperature coupling is on<br>Tcoupl = berendsen<br>
tau_t = 0.01 0.01<br>tc_grps = protein non-protein<br>ref_t = 300 300<br>; Pressure coupling is on<br>Pcoupl = berendsen<br>pcoupltype = isotropic<br>
tau_p = 0.5<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Generate velocites is on at 300 K.<br>gen_vel = yes<br>gen_temp = 300.0<br>gen_seed = 173529</div>
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<div>Thanking you</div>
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<div> With best regards</div>
<div> Anamika</div></div><br><br clear="all"><br>