Dear gromacs users:<br> I am using following mdp file as input for simulating the system with NVE ensemble. But when i check the 'Total energy',<br>it doesn't seems to remain constant and keep decreasing. I am also giving some part of my output. Thanks for your help <br>
Rama<br><br>title = Water box<br>DEFINE = -DFLEXIBLE<br>constraints = hbonds<br>constraint_algorithm = shake<br>integrator = md<br>dt = 0.001 ;<br>nsteps = 1500000 ;<br>
nstcomm = 100 <br>nstlist = 10<br>ns_type = grid<br>nstenergy = 5 <br>nstlog = 0 <br>nstvout = 5 <br>nstxout = 5 <br>nstxtcout = 0 <br>
xtc-precision = 100<br>nstfout = 0<br>coulombtype = shift<br>fourierspacing = 0.135<br>pme_order = 4<br>vdwtype = switch<br>rvdw = 1.0<br>rlist = 1.2<br>
rcoulomb = 1.0<br>pbc = xyz<br>fourier_nx = 0.0<br>fourier_ny = 0.0<br>fourier_nz = 0.0<br>;Berendsen temperature coupling is on<br><br>Tcoupl = no ; temperature bath (yes, no)<br>
tau_t = 0.1<br>tc-grps = system<br>ref_t = 200<br><br>;Berendsen Pressure coupling is on<br>pcoupl = no ; pressure bath (yes, no)<br>pcoupltype = isotropic<br>tau_p = 0.5<br>
compressibility = 4.5e-05<br>ref_p = 1.0<br><br>;Generate velocities is on at 300K<br>gen_vel = yes ; generate initial velocities<br>gen_temp = 300.0 ; initial temperature<br>gen_seed = 173529 ; random seed<br>
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------<br>Output:<br>"Total Energy" <br> 0.000000 -59821.300781<br>
0.005000 -59806.011719<br> 0.010000 -59790.937500<br> 0.015000 -59799.031250<br> 0.020000 -59803.445312<br> 0.025000 -59799.058594<br> 0.030000 -59803.445312<br> 0.035000 -59804.835938<br> 0.040000 -59801.652344<br>
0.045000 -59803.144531<br> 0.050000 -59804.605469<br> 0.055000 -59803.421875<br> 0.060000 -59806.074219<br> 0.065000 -59805.125000<br> 0.070000 -59803.632812<br> 0.075000 -59805.742188<br> 0.080000 -59807.140625<br>
0.085000 -59806.539062<br> 0.090000 -59806.328125<br> 0.095000 -59806.949219<br> 0.100000 -59807.351562<br> 0.105000 -59806.531250<br> 0.110000 -59806.894531<br> 0.115000 -59808.933594<br> 0.120000 -59808.585938<br>
0.125000 -59807.019531<br> 0.130000 -59808.171875<br> 0.135000 -59809.117188<br> 0.140000 -59808.242188<br> 0.145000 -59808.820312<br> 0.150000 -59808.750000<br> 0.155000 -59806.507812<br> 0.160000 -59808.839844<br>
0.165000 -59810.800781<br><br>