Date: Wed, 17 Jun 2009 18:00:46 +0100
Dear all,
According to Ross's advices, I updated my protocol and I still get
some problems to look at the water...
Here is my new Production :
MD Production
&cntrl
igb = 0, ntb = 2, ntpr = 250, ntwx = 500,
cut = 9.0,
tempi = 300.0, temp0 = 300.0,
ntt = 1, tautp = 5.0, taup = 5.0,
ntp = 1, imin = 0,
nstlim = 1000000, dt = 0.002,
ntc = 2, ntf = 2, tol = 0.00000001,
ntwr = 500, nscm = 2500,
irest = 1, ntx = 5, iwrap = 1,
nmropt = 1, ibelly = 0,
&end
&ewald
ew_type = 0, skinnb = 1.0, nbflag = 1, use_pme = 1, vdwmeth = 1,
&end
&wt
type='END',
&end
LISTOUT = POUT
DISANG = R2_restraint
Here is my ptraj input :
trajin R2.mdcrd
center :1-4 mass origin
image origin center familiar
trajout all.traj trajectory
You will find as attachment a screenshot of what I see... Contacts
look now fine but as you can see, I am having some troubles with the
box. Where does it come from? Is it a visualization problem or a
simulation one?
(image/png attachment: box_wat.png)
- text/plain attachment: ATT00003.txt
- text/plain attachment: ATT00004.txt
