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style="text-align:undefined;">Dear GROMACS users and developers,<br><br>I'm having trouble getting values for my 1/viscosity calculation which obtained from g_energy:<br><br>g_energy -f md1_vis.edr -o md1_vis_1perv.xvg<br><br><br>the output:<br><br>Statistics over 1000001 steps [ 0.0000 through 2000.0000 ps ], 1 data sets<br>All statistics are over 100001 points<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>1/Viscosity 0 0
0 0 (m s/kg)<br><br>gcq#310: "Shoot them in the back now" (The Ramones)<br><br><div> Have I done something wrong with my simulation? If that's the case, then this is my mdp parameter:<br><br>cpp = /lib/cpp<br>include = -I../top<br>integrator = md<br>dt = 0.002<br>nsteps = 10000<br>nstxout = 100<br>nstvout = 100<br>nstlog = 1000<br>nstenergy = 100<br>nstxtcout = 100<br>xtc_grps
= System <br>energygrps = System <br>nstlist = 10 <br>ns_type = grid<br><br>rlist = 1.0<br><br>; PME chosen as the best option to calculate viscosity ;<br>coulombtype = PME<br>rcoulomb = 1.0<br><br>rvdw = 1.4<br><br>pbc = xyz<br><br>tcoupl = berendsen<br>tc-grps = System <br>tau_t = 0.1<br><br>;
temperature supposed to set to 20*C @ 293.15 K as reference work ; <br>ref_t = 293.15<br><br>Pcoupl = no<br><br>gen_vel = yes<br>gen_temp = 298.15<br>gen_seed = 173529<br><br>constraints = none<br><br><br>; NEMD ;<br><br>acc_grps = system<br>accelerate = 0.1 0.0 0.0<br>cos_acceleration = 0.02<br><br><br>Any suggestion are most welcomed and thank you in advance!<br><br><br><br></div>MUHAMMAD ALIF MOHAMMAD LATIF<br>Laboratory of
Theoretical and Computational Chemistry<br>Department of Chemistry<br>Faculty of Science<br>Universiti Putra Malaysia<br>43400 UPM Serdang, Selangor<br>MALAYSIA<div><br></div>
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