I almost removed everything. I am generating initial velocity at 0.01 K
so the system should freeze. Its a dilute gas. But somehow I am getting
very large velocites i.e. very large KE of the whole system.<br>
<br>
here is my .mdp file.<br>
---------------------------------------<br>
integrator = md<br>
tinit = 0<br>
dt
= 0.001<br>
nsteps = 500000<br>
init_step = 0<br>
comm-mode = Linear<br>
nstcomm = 1<br>
comm-grps =<br>
niter = 20<br>
fcstep = 0<br>
nstxout = 0<br>
nstvout = 0<br>
nstfout = 0<br>
nstcheckpoint = 1000<br>
nstlog = 50<br>
nstenergy = 50<br>
nstxtcout = 50<br>
xtc-precision = 1000<br>
nstlist = 5<br>
ns_type = grid<br>
pbc
= xyz<br>
rlist = 4.50<br>
domain-decomposition = no<br>
<br>
coulombtype = Cut-off<br>
rcoulomb-switch = 0<br>
rcoulomb = 4.50<br>
epsilon-r = 1<br>
vdw-type = Cut-off<br>
rvdw-switch = 0<br>
rvdw
= 4.50<br>
DispCorr = no ;EnerPres<br>
table-extension = 1<br>
fourierspacing = 0.12<br>
fourier_nx = 0<br>
fourier_ny = 0<br>
fourier_nz = 0<br>
<br>
gb_algorithm = Still<br>
nstgbradii = 4.50<br>
rgbradii = 2<br>
gb_saltconc = 0<br>
implicit_solvent = No<br>
<br>
Tcoupl
= no ;berendsen<br>
Pcoupl
= no ;berendsen<br>
<br>
annealing = no<br>
<br>
gen_vel = yes<br>
gen_temp = 0.01<br>
gen_seed = 1993<br>
<br>
constraints = all-bonds<br>
constraint-algorithm = Lincs<br>
unconstrained-start = yes<br>
Shake-SOR = no<br>
shake-tol = 1e-04<br>
lincs-order = 4<br>
lincs-iter = 2<br>
morse = no<br>
<br>
disre = No<br>
disre-weighting = Conservative<br>
disre-mixed = no<br>
disre-fc = 1000<br>
disre-tau = 0<br>
nstdisreout = 100<br>
orire = no<br>
orire-fc = 0<br>
orire-tau = 0<br>
orire-fitgrp =<br>
nstorireout = 100<br>
dihre = No<br>
dihre-fc = 1000<br>
dihre-tau = 0<br>
nstdihreout = 100<br>
<br>
free-energy = no<br>
init-lambda = 0<br>
delta-lambda = 0<br>
sc-alpha = 0<br>
sc-sigma = 0.3<br>
<br>
cos-acceleration = 0<br>
----------------------------------------<br>
can you suggest some changes? what fault/error can you see?<br>
-<br>
karamyog.<br><br>