Hello. I am trying to calculate the self diffusion of
water at equilibrium (T=300K, P=1atm). I would like to run
molecular dynamics on a box of 216 water molecules and then
calculate the diffusion coefficient so I can compare the
results to the results I have gotten from another program.
I am a new AMBER user, but I have tried several of the
tutorials and I have been using the manual to get started.
I would appreciate any advice you can give. Here is where
I am so far. Feel free to tell me to start over from
scratch if that is best.
Following the methane tutorial, I have built a waterbox
using xleap:
edit WAT
saveoff WAT water216.lib
x=copy WAT
solvatebox x WATBOX216 10
saveamberparm x watbox.top watbox.crd
Then I want to run sander_classic -O \
-i mdin.in \
-p watbox.top \
-c watbox.crd \
-o mdout.out \
I attempted to draft an "mdin.in" file:
molecular dynamics run
&cntrl
imin=0, nmropt=0, ntx=1, irest=0,
ntrx=1, ntxo=1, ntpr=50, ntwr=50,
iwrap=0,
ntwx=50, ntwv=50, ntwe=50,
ntwxm=500, ntwvm=500, ntwem=500,
ioutfm=0, ntwprt=0,
ntf=1, ntb=2, dielc=1.0, igb=0,
ipol=0, n3b=5, nion=0,
cut = 8.0,
&end
&ewald
a=26.782, b=27.009, c=26.192,
&end
Any help would be greatly appreciated!!
Sincerely,
Gail
Received on Fri Oct 20 2000 - 18:55:38 PDT
