self diffusion of water at equilibrium T=300K P=1atm

From: gail louise dempsey <>
Date: Fri 20 Oct 2000 21:55:38 -0400 (Eastern Daylight Time)

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.crd

Then I want to run sander_classic -O \
                        -i \
                        -p \
                        -c watbox.crd \
                        -o mdout.out \

I attempted to draft an "" file:

molecular dynamics run
        imin=0, nmropt=0, ntx=1, irest=0,
        ntrx=1, ntxo=1, ntpr=50, ntwr=50,
        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,
 a=26.782, b=27.009, c=26.192,

Any help would be greatly appreciated!!

Received on Fri Oct 20 2000 - 18:55:38 PDT
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