Dear Mark:<br> Thanks for your suggestions. I did equilibration for about 500ps but still there is energy fluctuation exist (as give below). Is this deviation is acceptable for NVE ensemble or still i need to equilibrate the system for some more picosecond.<br>
<br>Energy Average RMSD Fluct. Drift Tot-Drift<br>-------------------------------------------------------------------------------<br>Total-Energy -17710.5 66.1524 2.39547 -0.458016 -229.008<br>
<br> <br>-----------------------<br>Rama<br><br><div class="gmail_quote">On Tue, Mar 30, 2010 at 11:15 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">On 31/03/2010 2:51 PM, Ramachandran G wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear gromacs users:<br>
I am using following mdp file as input for simulating the<br>
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<br>
</blockquote>
<br></div>
Thus, you are not yet in an NVE ensemble. Generating velocities is only an approximate process, and it takes at least several picoseconds for some observables to start converging to their ensemble-average values. So, equilibrate before you start collecting data!<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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>
</blockquote>
<br></div>
Don't simulate with flexible water and bond constraints. It's inconsistent.<br>
<br>
Mark<div><div></div><div class="h5"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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>
</blockquote></div></div><font color="#888888">
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